PDB Short entry for 3F2B HEADER TRANSFERASE/DNA 29-OCT-08 3F2B TITLE DNA POLYMERASE POLC FROM GEOBACILLUS KAUSTOPHILUS COMPLEX WITH DNA, TITLE 2 DGTP, MG AND ZN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-DIRECTED DNA POLYMERASE III ALPHA CHAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GKAPOLC, DELTA 1-227, DELTA 412-617; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*DCP*DAP*DGP*DTP*DGP*DAP*DGP*DAP*DCP*DGP*DGP*DGP*DCP*D COMPND 9 AP*DAP*DCP*DC)-3'; COMPND 10 CHAIN: P; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: DNA PRIMER STRAND; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-D(*DAP*DTP*DAP*DAP*DCP*DGP*DGP*DTP*DTP*DGP*DCP*DCP*DCP*D COMPND 15 GP*DTP*DCP*DTP*DCP*DAP*DCP*DTP*DG)-3'; COMPND 16 CHAIN: T; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: DNA TEMPLATE STRAND SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS KAUSTOPHILUS; SOURCE 3 ORGANISM_TAXID: 1462; SOURCE 4 GENE: GK1258, POLC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 OTHER_DETAILS: PRIMER STRAND SYNTHETIC OLIGONUCLEOTIDE; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: TEMPLATE STRAND SYNTHETIC OLIGONUCLEOTIDE KEYWDS DNA POLYMERASE C, DNA POLYMERASE III, TERNARY COMPLEX, PROTEIN-DNA KEYWDS 2 COMPLEX, REPLICATIVE DNA POLYMERASE, DNA REPLICATION, DNA-DIRECTED KEYWDS 3 DNA POLYMERASE, EXONUCLEASE, HYDROLASE, NUCLEASE, KEYWDS 4 NUCLEOTIDYLTRANSFERASE, TRANSFERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.R.DAVIES,R.J.EVANS,J.M.BULLARD,J.CHRISTENSEN,L.S.GREEN,J.W.GUILES, AUTHOR 2 W.K.RIBBLE,N.JANJIC,T.C.JARVIS REVDAT 5 27-DEC-23 3F2B 1 REMARK SEQADV LINK REVDAT 4 26-JUL-17 3F2B 1 SOURCE REMARK REVDAT 3 13-JUL-11 3F2B 1 VERSN REVDAT 2 02-MAR-10 3F2B 1 REMARK REVDAT 1 20-JAN-09 3F2B 0 JRNL AUTH R.J.EVANS,D.R.DAVIES,J.M.BULLARD,J.CHRISTENSEN,L.S.GREEN, JRNL AUTH 2 J.W.GUILES,J.D.PATA,W.K.RIBBLE,N.JANJIC,T.C.JARVIS JRNL TITL STRUCTURE OF POLC REVEALS UNIQUE DNA BINDING AND FIDELITY JRNL TITL 2 DETERMINANTS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 20695 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 19106298 JRNL DOI 10.1073/PNAS.0809989106 REMARK 2 REMARK 2 RESOLUTION. 2.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0069 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 59703 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3017 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.39 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.45 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3979 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.4060 REMARK 3 BIN FREE R VALUE SET COUNT : 209 REMARK 3 BIN FREE R VALUE : 0.4500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7815 REMARK 3 NUCLEIC ACID ATOMS : 631 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 95 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.77000 REMARK 3 B22 (A**2) : 2.29000 REMARK 3 B33 (A**2) : -0.52000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.345 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.259 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.203 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.074 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8731 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11954 ; 1.609 ; 2.068 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 990 ; 6.088 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 362 ;38.326 ;24.254 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1398 ;20.471 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 47 ;20.495 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1334 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6347 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4945 ; 0.512 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 8003 ; 0.981 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3786 ; 1.593 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3951 ; 2.553 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 233 A 331 REMARK 3 ORIGIN FOR THE GROUP (A): 38.2807 -12.1426 -16.1455 REMARK 3 T TENSOR REMARK 3 T11: -0.0716 T22: -0.0759 REMARK 3 T33: -0.1267 T12: -0.0459 REMARK 3 T13: 0.0062 T23: 0.0776 REMARK 3 L TENSOR REMARK 3 L11: 6.2547 L22: 3.4847 REMARK 3 L33: 3.3164 L12: -2.1880 REMARK 3 L13: 1.8214 L23: -2.2223 REMARK 3 S TENSOR REMARK 3 S11: 0.1029 S12: -0.0269 S13: -0.1923 REMARK 3 S21: -0.2610 S22: 0.1508 S23: 0.1999 REMARK 3 S31: 0.2261 S32: 0.0005 S33: -0.2536 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 332 A 411 REMARK 3 ORIGIN FOR THE GROUP (A): 38.5900 4.3948 -46.4176 REMARK 3 T TENSOR REMARK 3 T11: 0.1107 T22: -0.0337 REMARK 3 T33: -0.1031 T12: -0.1935 REMARK 3 T13: -0.0693 T23: 0.0333 REMARK 3 L TENSOR REMARK 3 L11: 0.8618 L22: 1.9122 REMARK 3 L33: 2.2246 L12: 0.5266 REMARK 3 L13: -0.3795 L23: 0.0043 REMARK 3 S TENSOR REMARK 3 S11: -0.1189 S12: -0.0029 S13: -0.1036 REMARK 3 S21: -0.1561 S22: 0.3534 S23: -0.1164 REMARK 3 S31: 0.5792 S32: -0.3697 S33: -0.2345 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 619 A 708 REMARK 3 ORIGIN FOR THE GROUP (A): 28.1327 12.3487 -57.2261 REMARK 3 T TENSOR REMARK 3 T11: -0.0555 T22: 0.3352 REMARK 3 T33: -0.1750 T12: -0.3262 REMARK 3 T13: -0.1219 T23: 0.1301 REMARK 3 L TENSOR REMARK 3 L11: 1.2050 L22: 3.0102 REMARK 3 L33: 3.2898 L12: -0.1327 REMARK 3 L13: 0.2080 L23: 0.5967 REMARK 3 S TENSOR REMARK 3 S11: -0.0954 S12: 0.3297 S13: 0.1666 REMARK 3 S21: -0.3685 S22: 0.2305 S23: 0.2198 REMARK 3 S31: 0.3546 S32: -1.0761 S33: -0.1351 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 716 A 772 REMARK 3 ORIGIN FOR THE GROUP (A): 23.9795 -1.6722 -49.0967 REMARK 3 T TENSOR REMARK 3 T11: 0.1967 T22: 0.3966 REMARK 3 T33: -0.0469 T12: -0.5306 REMARK 3 T13: -0.1490 T23: 0.1297 REMARK 3 L TENSOR REMARK 3 L11: 0.5410 L22: 1.2186 REMARK 3 L33: 7.2598 L12: -0.0845 REMARK 3 L13: -1.9341 L23: 0.9472 REMARK 3 S TENSOR REMARK 3 S11: -0.2886 S12: 0.5237 S13: -0.1452 REMARK 3 S21: -0.2767 S22: 0.3494 S23: 0.1930 REMARK 3 S31: 0.8801 S32: -1.6472 S33: -0.0608 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 773 A 825 REMARK 3 ORIGIN FOR THE GROUP (A): 38.9952 1.0510 -53.3966 REMARK 3 T TENSOR REMARK 3 T11: 0.1489 T22: -0.0112 REMARK 3 T33: -0.1542 T12: -0.2690 REMARK 3 T13: -0.0292 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.8272 L22: 1.7082 REMARK 3 L33: 1.5743 L12: 0.8358 REMARK 3 L13: 0.3859 L23: 0.3817 REMARK 3 S TENSOR REMARK 3 S11: -0.1512 S12: 0.1995 S13: -0.1771 REMARK 3 S21: -0.3276 S22: 0.4086 S23: -0.4038 REMARK 3 S31: 0.5009 S32: -0.3021 S33: -0.2574 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 826 A 996 REMARK 3 ORIGIN FOR THE GROUP (A): 55.6995 44.7092 -25.8983 REMARK 3 T TENSOR REMARK 3 T11: -0.0145 T22: -0.0955 REMARK 3 T33: -0.0176 T12: -0.0095 REMARK 3 T13: 0.0457 T23: -0.0080 REMARK 3 L TENSOR REMARK 3 L11: 1.3384 L22: 0.7591 REMARK 3 L33: 2.5441 L12: 0.3636 REMARK 3 L13: 0.3033 L23: -0.1983 REMARK 3 S TENSOR REMARK 3 S11: 0.1305 S12: 0.0219 S13: 0.0924 REMARK 3 S21: 0.0496 S22: -0.0135 S23: -0.0852 REMARK 3 S31: -0.4934 S32: 0.2139 S33: -0.1170 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 997 A 1122 REMARK 3 ORIGIN FOR THE GROUP (A): 34.4785 24.5086 -31.5013 REMARK 3 T TENSOR REMARK 3 T11: -0.1042 T22: 0.0573 REMARK 3 T33: -0.0228 T12: 0.0172 REMARK 3 T13: -0.0011 T23: 0.0789 REMARK 3 L TENSOR REMARK 3 L11: 0.2318 L22: 0.7185 REMARK 3 L33: 0.2991 L12: -0.0448 REMARK 3 L13: 0.0487 L23: -0.1130 REMARK 3 S TENSOR REMARK 3 S11: 0.0030 S12: 0.0079 S13: 0.0932 REMARK 3 S21: 0.0014 S22: 0.2034 S23: 0.1482 REMARK 3 S31: 0.0118 S32: -0.2095 S33: -0.2064 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1123 A 1307 REMARK 3 ORIGIN FOR THE GROUP (A): 51.5789 28.5676 -9.9096 REMARK 3 T TENSOR REMARK 3 T11: -0.0617 T22: -0.0439 REMARK 3 T33: -0.0551 T12: 0.0342 REMARK 3 T13: -0.0175 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 1.5735 L22: 0.3185 REMARK 3 L33: 1.2777 L12: -0.4002 REMARK 3 L13: -0.2795 L23: -0.0926 REMARK 3 S TENSOR REMARK 3 S11: 0.0315 S12: -0.1152 S13: 0.0230 REMARK 3 S21: 0.0855 S22: 0.0522 S23: -0.0693 REMARK 3 S31: 0.0964 S32: 0.0830 S33: -0.0837 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1308 A 1359 REMARK 3 ORIGIN FOR THE GROUP (A): 25.6167 30.3168 -1.0801 REMARK 3 T TENSOR REMARK 3 T11: -0.0634 T22: 0.0290 REMARK 3 T33: -0.0629 T12: 0.0521 REMARK 3 T13: 0.0170 T23: 0.0786 REMARK 3 L TENSOR REMARK 3 L11: 2.8411 L22: 4.5791 REMARK 3 L33: 1.4698 L12: -2.6449 REMARK 3 L13: -0.6712 L23: -0.5603 REMARK 3 S TENSOR REMARK 3 S11: 0.0434 S12: -0.2805 S13: -0.3632 REMARK 3 S21: 0.0951 S22: 0.0085 S23: 0.2056 REMARK 3 S31: 0.2194 S32: -0.3591 S33: -0.0520 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1360 A 1444 REMARK 3 ORIGIN FOR THE GROUP (A): 9.0215 45.1770 -12.4536 REMARK 3 T TENSOR REMARK 3 T11: -0.0401 T22: 0.0997 REMARK 3 T33: -0.0729 T12: 0.1150 REMARK 3 T13: 0.0531 T23: 0.0218 REMARK 3 L TENSOR REMARK 3 L11: 7.8110 L22: 0.4371 REMARK 3 L33: 0.0856 L12: -1.8416 REMARK 3 L13: 0.6514 L23: -0.1631 REMARK 3 S TENSOR REMARK 3 S11: 0.0908 S12: 0.4082 S13: 0.1689 REMARK 3 S21: -0.1412 S22: -0.1822 S23: 0.0009 REMARK 3 S31: -0.0908 S32: -0.0605 S33: 0.0915 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : P 5 P 17 REMARK 3 RESIDUE RANGE : T 1 T 18 REMARK 3 ORIGIN FOR THE GROUP (A): 23.6307 24.2914 -19.8596 REMARK 3 T TENSOR REMARK 3 T11: -0.0927 T22: 0.2076 REMARK 3 T33: 0.1084 T12: 0.0397 REMARK 3 T13: 0.0458 T23: 0.0185 REMARK 3 L TENSOR REMARK 3 L11: 1.5170 L22: 0.8953 REMARK 3 L33: 1.0484 L12: 0.5047 REMARK 3 L13: 0.4031 L23: 0.9615 REMARK 3 S TENSOR REMARK 3 S11: -0.1504 S12: 0.0227 S13: 0.1239 REMARK 3 S21: 0.0688 S22: -0.1306 S23: 0.3199 REMARK 3 S31: -0.0795 S32: -0.4796 S33: 0.2810 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3F2B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000050057. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.30 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59793 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 43.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.82400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 2000 MME, 0.1M PHOSPHATE- REMARK 280 CITRATE, 200MM LITHIUM SULFATE, PH 5.3, VAPOR DIFFUSION, PH 5.30, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 92.26200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 92.26200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 58.08700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 70.39650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 58.08700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 70.39650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 92.26200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 58.08700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 70.39650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 92.26200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 58.08700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 70.39650 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P, T REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 227 REMARK 465 ARG A 228 REMARK 465 ASP A 229 REMARK 465 GLU A 230 REMARK 465 GLU A 231 REMARK 465 PRO A 232 REMARK 465 GLY A 412 REMARK 465 VAL A 413 REMARK 465 PRO A 414 REMARK 465 ILE A 415 REMARK 465 ALA A 416 REMARK 465 TYR A 417 REMARK 465 ASN A 418 REMARK 465 GLU A 419 REMARK 465 THR A 420 REMARK 465 HIS A 421 REMARK 465 ARG A 422 REMARK 465 ARG A 423 REMARK 465 LEU A 424 REMARK 465 GLY A 425 REMARK 465 SER A 426 REMARK 465 GLY A 427 REMARK 465 SER A 428 REMARK 465 GLY A 429 REMARK 465 LEU A 679 REMARK 465 ILE A 680 REMARK 465 GLN A 681 REMARK 465 LYS A 682 REMARK 465 ALA A 683 REMARK 465 PRO A 684 REMARK 465 GLU A 685 REMARK 465 GLU A 686 REMARK 465 ILE A 709 REMARK 465 GLU A 710 REMARK 465 MET A 711 REMARK 465 ASP A 712 REMARK 465 SER A 1445 REMARK 465 GLY A 1446 REMARK 465 GLY A 1447 REMARK 465 HIS A 1448 REMARK 465 HIS A 1449 REMARK 465 HIS A 1450 REMARK 465 HIS A 1451 REMARK 465 HIS A 1452 REMARK 465 HIS A 1453 REMARK 465 HIS A 1454 REMARK 465 HIS A 1455 REMARK 465 DC P 1 REMARK 465 DA P 2 REMARK 465 DG P 3 REMARK 465 DT P 4 REMARK 465 DA T 19 REMARK 465 DC T 20 REMARK 465 DT T 21 REMARK 465 DG T 22 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 305 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 330 CG OD1 ND2 REMARK 470 GLU A 340 CG CD OE1 OE2 REMARK 470 ARG A 648 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 706 CG CD CE NZ REMARK 470 LEU A 708 CG CD1 CD2 REMARK 470 TYR A 713 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 VAL A 714 CG1 CG2 REMARK 470 LYS A 715 CG CD CE NZ REMARK 470 ARG A 770 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 771 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 969 CG OD1 OD2 REMARK 470 DC P 17 O3' REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 SG CYS A 947 OG1 THR A 949 1.96 REMARK 500 NH1 ARG A 654 OE2 GLU A 674 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 688 CG GLU A 688 CD 0.108 REMARK 500 GLU A 717 CD GLU A 717 OE1 0.071 REMARK 500 GLU A 718 CD GLU A 718 OE1 -0.070 REMARK 500 DT T 8 O4' DT T 8 C4' -0.100 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 793 C - N - CA ANGL. DEV. = 9.1 DEGREES REMARK 500 VAL A 896 CB - CA - C ANGL. DEV. = -11.7 DEGREES REMARK 500 DG P 5 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DA P 6 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG P 7 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG P 7 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA P 8 C3' - O3' - P ANGL. DEV. = -7.5 DEGREES REMARK 500 DG P 12 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC P 13 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC P 13 C5 - C4 - N4 ANGL. DEV. = -5.0 DEGREES REMARK 500 DC P 16 C5' - C4' - O4' ANGL. DEV. = 7.3 DEGREES REMARK 500 DC P 16 O4' - C1' - N1 ANGL. DEV. = 10.3 DEGREES REMARK 500 DC P 17 N1 - C1' - C2' ANGL. DEV. = 8.8 DEGREES REMARK 500 DC P 17 O4' - C1' - N1 ANGL. DEV. = -4.7 DEGREES REMARK 500 DC P 17 N3 - C4 - N4 ANGL. DEV. = -5.9 DEGREES REMARK 500 DC P 17 C5 - C4 - N4 ANGL. DEV. = 4.5 DEGREES REMARK 500 DA T 3 O4' - C1' - N9 ANGL. DEV. = -4.3 DEGREES REMARK 500 DC T 5 O4' - C1' - N1 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT T 8 O5' - P - OP2 ANGL. DEV. = -5.8 DEGREES REMARK 500 DT T 8 C5' - C4' - C3' ANGL. DEV. = 8.6 DEGREES REMARK 500 DT T 8 C5' - C4' - O4' ANGL. DEV. = 8.8 DEGREES REMARK 500 DT T 8 N1 - C1' - C2' ANGL. DEV. = -24.7 DEGREES REMARK 500 DT T 8 O4' - C1' - N1 ANGL. DEV. = 11.0 DEGREES REMARK 500 DT T 8 C5 - C4 - O4 ANGL. DEV. = -4.5 DEGREES REMARK 500 DC T 13 C6 - N1 - C2 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC T 13 C2 - N3 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 DC T 13 N3 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC T 13 C5 - C6 - N1 ANGL. DEV. = -3.6 DEGREES REMARK 500 DT T 15 C3' - O3' - P ANGL. DEV. = 10.5 DEGREES REMARK 500 DC T 16 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC T 16 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 DT T 17 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 DT T 17 C4 - C5 - C7 ANGL. DEV. = 4.2 DEGREES REMARK 500 DT T 17 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 DC T 18 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 243 128.36 -171.20 REMARK 500 TYR A 274 1.51 81.88 REMARK 500 ASN A 276 -161.49 -166.25 REMARK 500 ASN A 330 47.41 24.23 REMARK 500 ARG A 332 127.53 -39.25 REMARK 500 GLN A 353 114.16 -35.07 REMARK 500 VAL A 357 -23.64 -140.51 REMARK 500 ALA A 381 -5.34 65.71 REMARK 500 ILE A 643 -75.54 -116.68 REMARK 500 HIS A 647 -80.06 -101.63 REMARK 500 CYS A 670 -175.17 -37.22 REMARK 500 PRO A 707 98.80 -55.93 REMARK 500 LEU A 747 -70.83 -62.07 REMARK 500 PRO A 767 55.28 26.90 REMARK 500 LYS A 923 -1.49 72.43 REMARK 500 PRO A 945 27.21 -73.67 REMARK 500 ARG A 946 -51.54 -127.71 REMARK 500 ASP A 969 31.36 -94.58 REMARK 500 ASN A1025 49.09 39.90 REMARK 500 MET A1061 -167.34 -114.75 REMARK 500 GLN A1070 -170.00 -175.66 REMARK 500 ALA A1073 14.68 55.55 REMARK 500 HIS A1091 -36.54 -39.58 REMARK 500 ASP A1125 20.16 -144.43 REMARK 500 CYS A1148 145.14 -171.98 REMARK 500 GLU A1157 -62.11 70.62 REMARK 500 TRP A1191 -69.28 -107.85 REMARK 500 ASN A1194 -106.36 -139.34 REMARK 500 GLU A1405 160.25 -45.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 4 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 919 SG REMARK 620 2 CYS A 922 SG 110.7 REMARK 620 3 CYS A 944 SG 110.9 100.6 REMARK 620 4 CYS A 947 SG 76.5 130.0 123.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 5 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 973 OD2 REMARK 620 2 ASP A 975 OD2 88.9 REMARK 620 3 DGT A1456 O2A 90.3 100.1 REMARK 620 4 DGT A1456 O2G 86.1 164.9 94.1 REMARK 620 5 DGT A1456 O1B 163.4 95.0 104.8 86.1 REMARK 620 6 HOH A1457 O 79.4 79.7 169.7 85.4 85.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 6 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 92 O REMARK 620 2 GLU A 405 OE1 92.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 7 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 92 O REMARK 620 2 HIS A 346 NE2 143.4 REMARK 620 3 HIS A 348 NE2 106.9 107.8 REMARK 620 4 GLU A 405 OE1 81.1 80.7 101.6 REMARK 620 5 ASN A 743 OD1 98.3 91.4 92.8 165.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGT A1456 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3F2C RELATED DB: PDB REMARK 900 SAME PROTEIN-DNA COMPLEX CRYSTALLIZED WITH MN REMARK 900 RELATED ID: 3F2D RELATED DB: PDB REMARK 900 SAME PROTEIN-DNA COMPLEX CRYSTALLIZED WITH COMPLEX DGTP, MN AND ZN DBREF 3F2B A 228 424 UNP Q5L0J3 Q5L0J3_GEOKA 227 423 DBREF 3F2B A 618 1444 UNP Q5L0J3 Q5L0J3_GEOKA 618 1444 DBREF 3F2B P 1 17 PDB 3F2B 3F2B 1 17 DBREF 3F2B T 1 22 PDB 3F2B 3F2B 1 22 SEQADV 3F2B MET A 227 UNP Q5L0J3 EXPRESSION TAG SEQADV 3F2B GLY A 425 UNP Q5L0J3 LINKER SEQADV 3F2B SER A 426 UNP Q5L0J3 LINKER SEQADV 3F2B GLY A 427 UNP Q5L0J3 LINKER SEQADV 3F2B SER A 428 UNP Q5L0J3 LINKER SEQADV 3F2B GLY A 429 UNP Q5L0J3 LINKER SEQADV 3F2B SER A 1445 UNP Q5L0J3 EXPRESSION TAG SEQADV 3F2B GLY A 1446 UNP Q5L0J3 EXPRESSION TAG SEQADV 3F2B GLY A 1447 UNP Q5L0J3 EXPRESSION TAG SEQADV 3F2B HIS A 1448 UNP Q5L0J3 EXPRESSION TAG SEQADV 3F2B HIS A 1449 UNP Q5L0J3 EXPRESSION TAG SEQADV 3F2B HIS A 1450 UNP Q5L0J3 EXPRESSION TAG SEQADV 3F2B HIS A 1451 UNP Q5L0J3 EXPRESSION TAG SEQADV 3F2B HIS A 1452 UNP Q5L0J3 EXPRESSION TAG SEQADV 3F2B HIS A 1453 UNP Q5L0J3 EXPRESSION TAG SEQADV 3F2B HIS A 1454 UNP Q5L0J3 EXPRESSION TAG SEQADV 3F2B HIS A 1455 UNP Q5L0J3 EXPRESSION TAG SEQRES 1 A 1041 MET ARG ASP GLU GLU PRO VAL ARG ARG LEU GLU THR ILE SEQRES 2 A 1041 VAL GLU GLU GLU ARG ARG VAL VAL VAL GLN GLY TYR VAL SEQRES 3 A 1041 PHE ASP ALA GLU VAL SER GLU LEU LYS SER GLY ARG THR SEQRES 4 A 1041 LEU LEU THR MET LYS ILE THR ASP TYR THR ASN SER ILE SEQRES 5 A 1041 LEU VAL LYS MET PHE SER ARG ASP LYS GLU ASP ALA GLU SEQRES 6 A 1041 LEU MET SER GLY VAL LYS LYS GLY MET TRP VAL LYS VAL SEQRES 7 A 1041 ARG GLY SER VAL GLN ASN ASP THR PHE VAL ARG ASP LEU SEQRES 8 A 1041 VAL ILE ILE ALA ASN ASP LEU ASN GLU ILE ALA ALA ASN SEQRES 9 A 1041 GLU ARG GLN ASP THR ALA PRO GLU GLY GLU LYS ARG VAL SEQRES 10 A 1041 GLU LEU HIS LEU HIS THR PRO MET SER GLN MET ASP ALA SEQRES 11 A 1041 VAL THR SER VAL THR LYS LEU ILE GLU GLN ALA LYS LYS SEQRES 12 A 1041 TRP GLY HIS PRO ALA ILE ALA VAL THR ASP HIS ALA VAL SEQRES 13 A 1041 VAL GLN SER PHE PRO GLU ALA TYR SER ALA ALA LYS LYS SEQRES 14 A 1041 HIS GLY MET LYS VAL ILE TYR GLY LEU GLU ALA ASN ILE SEQRES 15 A 1041 VAL ASP ASP GLY VAL PRO ILE ALA TYR ASN GLU THR HIS SEQRES 16 A 1041 ARG ARG LEU GLY SER GLY SER GLY PRO PHE HIS VAL THR SEQRES 17 A 1041 LEU LEU ALA GLN ASN GLU THR GLY LEU LYS ASN LEU PHE SEQRES 18 A 1041 LYS LEU VAL SER LEU SER HIS ILE GLN TYR PHE HIS ARG SEQRES 19 A 1041 VAL PRO ARG ILE PRO ARG SER VAL LEU VAL LYS HIS ARG SEQRES 20 A 1041 ASP GLY LEU LEU VAL GLY SER GLY CYS ASP LYS GLY GLU SEQRES 21 A 1041 LEU PHE ASP ASN LEU ILE GLN LYS ALA PRO GLU GLU VAL SEQRES 22 A 1041 GLU ASP ILE ALA ARG PHE TYR ASP PHE LEU GLU VAL HIS SEQRES 23 A 1041 PRO PRO ASP VAL TYR LYS PRO LEU ILE GLU MET ASP TYR SEQRES 24 A 1041 VAL LYS ASP GLU GLU MET ILE LYS ASN ILE ILE ARG SER SEQRES 25 A 1041 ILE VAL ALA LEU GLY GLU LYS LEU ASP ILE PRO VAL VAL SEQRES 26 A 1041 ALA THR GLY ASN VAL HIS TYR LEU ASN PRO GLU ASP LYS SEQRES 27 A 1041 ILE TYR ARG LYS ILE LEU ILE HIS SER GLN GLY GLY ALA SEQRES 28 A 1041 ASN PRO LEU ASN ARG HIS GLU LEU PRO ASP VAL TYR PHE SEQRES 29 A 1041 ARG THR THR ASN GLU MET LEU ASP CYS PHE SER PHE LEU SEQRES 30 A 1041 GLY PRO GLU LYS ALA LYS GLU ILE VAL VAL ASP ASN THR SEQRES 31 A 1041 GLN LYS ILE ALA SER LEU ILE GLY ASP VAL LYS PRO ILE SEQRES 32 A 1041 LYS ASP GLU LEU TYR THR PRO ARG ILE GLU GLY ALA ASP SEQRES 33 A 1041 GLU GLU ILE ARG GLU MET SER TYR ARG ARG ALA LYS GLU SEQRES 34 A 1041 ILE TYR GLY ASP PRO LEU PRO LYS LEU VAL GLU GLU ARG SEQRES 35 A 1041 LEU GLU LYS GLU LEU LYS SER ILE ILE GLY HIS GLY PHE SEQRES 36 A 1041 ALA VAL ILE TYR LEU ILE SER HIS LYS LEU VAL LYS LYS SEQRES 37 A 1041 SER LEU ASP ASP GLY TYR LEU VAL GLY SER ARG GLY SER SEQRES 38 A 1041 VAL GLY SER SER PHE VAL ALA THR MET THR GLU ILE THR SEQRES 39 A 1041 GLU VAL ASN PRO LEU PRO PRO HIS TYR VAL CYS PRO ASN SEQRES 40 A 1041 CYS LYS HIS SER GLU PHE PHE ASN ASP GLY SER VAL GLY SEQRES 41 A 1041 SER GLY PHE ASP LEU PRO ASP LYS ASN CYS PRO ARG CYS SEQRES 42 A 1041 GLY THR LYS TYR LYS LYS ASP GLY HIS ASP ILE PRO PHE SEQRES 43 A 1041 GLU THR PHE LEU GLY PHE LYS GLY ASP LYS VAL PRO ASP SEQRES 44 A 1041 ILE ASP LEU ASN PHE SER GLY GLU TYR GLN PRO ARG ALA SEQRES 45 A 1041 HIS ASN TYR THR LYS VAL LEU PHE GLY GLU ASP ASN VAL SEQRES 46 A 1041 TYR ARG ALA GLY THR ILE GLY THR VAL ALA ASP LYS THR SEQRES 47 A 1041 ALA TYR GLY PHE VAL LYS ALA TYR ALA SER ASP HIS ASN SEQRES 48 A 1041 LEU GLU LEU ARG GLY ALA GLU ILE ASP ARG LEU ALA ALA SEQRES 49 A 1041 GLY CYS THR GLY VAL LYS ARG THR THR GLY GLN HIS PRO SEQRES 50 A 1041 GLY GLY ILE ILE VAL VAL PRO ASP TYR MET GLU ILE TYR SEQRES 51 A 1041 ASP PHE THR PRO ILE GLN TYR PRO ALA ASP ASP THR SER SEQRES 52 A 1041 SER GLU TRP ARG THR THR HIS PHE ASP PHE HIS SER ILE SEQRES 53 A 1041 HIS ASP ASN LEU LEU LYS LEU ASP ILE LEU GLY HIS ASP SEQRES 54 A 1041 ASP PRO THR VAL ILE ARG MET LEU GLN ASP LEU SER GLY SEQRES 55 A 1041 ILE ASP PRO LYS THR ILE PRO THR ASP ASP PRO ASP VAL SEQRES 56 A 1041 MET GLY ILE PHE SER SER THR GLU PRO LEU GLY VAL THR SEQRES 57 A 1041 PRO GLU GLN ILE MET CYS ASN VAL GLY THR ILE GLY ILE SEQRES 58 A 1041 PRO GLU PHE GLY THR ARG PHE VAL ARG GLN MET LEU GLU SEQRES 59 A 1041 GLU THR ARG PRO LYS THR PHE SER GLU LEU VAL GLN ILE SEQRES 60 A 1041 SER GLY LEU SER HIS GLY THR ASP VAL TRP LEU GLY ASN SEQRES 61 A 1041 ALA GLN GLU LEU ILE GLN ASN GLY THR CYS THR LEU SER SEQRES 62 A 1041 GLU VAL ILE GLY CYS ARG ASP ASP ILE MET VAL TYR LEU SEQRES 63 A 1041 ILE TYR ARG GLY LEU GLU PRO SER LEU ALA PHE LYS ILE SEQRES 64 A 1041 MET GLU SER VAL ARG LYS GLY LYS GLY LEU THR PRO GLU SEQRES 65 A 1041 PHE GLU ALA GLU MET ARG LYS HIS ASP VAL PRO GLU TRP SEQRES 66 A 1041 TYR ILE ASP SER CYS LYS LYS ILE LYS TYR MET PHE PRO SEQRES 67 A 1041 LYS ALA HIS ALA ALA ALA TYR VAL LEU MET ALA VAL ARG SEQRES 68 A 1041 ILE ALA TYR PHE LYS VAL HIS HIS PRO LEU LEU TYR TYR SEQRES 69 A 1041 ALA SER TYR PHE THR VAL ARG ALA GLU ASP PHE ASP LEU SEQRES 70 A 1041 ASP ALA MET ILE LYS GLY SER ALA ALA ILE ARG LYS ARG SEQRES 71 A 1041 ILE GLU GLU ILE ASN ALA LYS GLY ILE GLN ALA THR ALA SEQRES 72 A 1041 LYS GLU LYS SER LEU LEU THR VAL LEU GLU VAL ALA LEU SEQRES 73 A 1041 GLU MET CYS GLU ARG GLY PHE SER PHE LYS ASN ILE ASP SEQRES 74 A 1041 LEU TYR ARG SER GLN ALA THR GLU PHE VAL ILE ASP GLY SEQRES 75 A 1041 ASN SER LEU ILE PRO PRO PHE ASN ALA ILE PRO GLY LEU SEQRES 76 A 1041 GLY THR ASN VAL ALA GLN ALA ILE VAL ARG ALA ARG GLU SEQRES 77 A 1041 GLU GLY GLU PHE LEU SER LYS GLU ASP LEU GLN GLN ARG SEQRES 78 A 1041 GLY LYS LEU SER LYS THR LEU LEU GLU TYR LEU GLU SER SEQRES 79 A 1041 ARG GLY CYS LEU ASP SER LEU PRO ASP HIS ASN GLN LEU SEQRES 80 A 1041 SER LEU PHE SER GLY GLY HIS HIS HIS HIS HIS HIS HIS SEQRES 81 A 1041 HIS SEQRES 1 P 17 DC DA DG DT DG DA DG DA DC DG DG DG DC SEQRES 2 P 17 DA DA DC DC SEQRES 1 T 22 DA DT DA DA DC DG DG DT DT DG DC DC DC SEQRES 2 T 22 DG DT DC DT DC DA DC DT DG HET PO4 A 1 5 HET PO4 A 2 5 HET PO4 A 3 5 HET ZN A 4 1 HET MG A 5 1 HET MG A 6 1 HET MG A 7 1 HET DGT A1456 31 HETNAM PO4 PHOSPHATE ION HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE FORMUL 4 PO4 3(O4 P 3-) FORMUL 7 ZN ZN 2+ FORMUL 8 MG 3(MG 2+) FORMUL 11 DGT C10 H16 N5 O13 P3 FORMUL 12 HOH *95(H2 O) HELIX 1 1 ARG A 235 ILE A 239 5 5 HELIX 2 2 ASP A 286 GLY A 295 1 10 HELIX 3 3 SER A 359 TRP A 370 1 12 HELIX 4 4 SER A 385 GLY A 397 1 13 HELIX 5 5 ASN A 627 ILE A 643 1 17 HELIX 6 6 ARG A 654 HIS A 660 1 7 HELIX 7 7 ILE A 690 TYR A 694 5 5 HELIX 8 8 PRO A 701 LYS A 706 5 6 HELIX 9 9 ASP A 716 LEU A 734 1 19 HELIX 10 10 ASN A 748 GLU A 750 5 3 HELIX 11 11 ASP A 751 SER A 761 1 11 HELIX 12 12 GLN A 762 ASN A 766 5 5 HELIX 13 13 THR A 780 SER A 789 1 10 HELIX 14 14 LEU A 791 VAL A 801 1 11 HELIX 15 15 VAL A 801 LEU A 810 1 10 HELIX 16 16 GLY A 828 GLY A 846 1 19 HELIX 17 17 PRO A 850 HIS A 867 1 18 HELIX 18 18 PHE A 869 ASP A 886 1 18 HELIX 19 19 GLY A 894 SER A 898 5 5 HELIX 20 20 SER A 899 THR A 905 1 7 HELIX 21 21 SER A 935 LEU A 939 5 5 HELIX 22 22 PHE A 960 GLY A 965 1 6 HELIX 23 23 TYR A 982 GLY A 995 1 14 HELIX 24 24 ALA A 1009 HIS A 1024 1 16 HELIX 25 25 ARG A 1029 THR A 1041 1 13 HELIX 26 26 GLU A 1062 PHE A 1066 5 5 HELIX 27 27 TYR A 1071 ASP A 1075 5 5 HELIX 28 28 PHE A 1087 HIS A 1091 1 5 HELIX 29 29 ASP A 1103 GLY A 1116 1 14 HELIX 30 30 ASP A 1118 ILE A 1122 5 5 HELIX 31 31 ASP A 1126 ILE A 1132 1 7 HELIX 32 32 THR A 1136 GLY A 1140 5 5 HELIX 33 33 THR A 1142 MET A 1147 1 6 HELIX 34 34 THR A 1160 ARG A 1171 1 12 HELIX 35 35 THR A 1174 SER A 1185 1 12 HELIX 36 36 ASN A 1194 ASN A 1201 1 8 HELIX 37 37 THR A 1205 VAL A 1209 5 5 HELIX 38 38 CYS A 1212 ARG A 1223 1 12 HELIX 39 39 GLU A 1226 ARG A 1238 1 13 HELIX 40 40 THR A 1244 HIS A 1254 1 11 HELIX 41 41 PRO A 1257 ILE A 1267 1 11 HELIX 42 42 PRO A 1272 HIS A 1293 1 22 HELIX 43 43 HIS A 1293 ARG A 1305 1 13 HELIX 44 44 ASP A 1310 GLY A 1317 1 8 HELIX 45 45 GLY A 1317 LYS A 1331 1 15 HELIX 46 46 GLY A 1332 ALA A 1335 5 4 HELIX 47 47 THR A 1336 ARG A 1355 1 20 HELIX 48 48 PRO A 1382 ILE A 1386 5 5 HELIX 49 49 GLY A 1390 GLU A 1403 1 14 HELIX 50 50 SER A 1408 LYS A 1417 1 10 HELIX 51 51 SER A 1419 ARG A 1429 1 11 SHEET 1 A 6 GLU A 243 GLU A 259 0 SHEET 2 A 6 THR A 265 THR A 272 -1 O THR A 268 N GLU A 256 SHEET 3 A 6 SER A 277 PHE A 283 -1 O VAL A 280 N MET A 269 SHEET 4 A 6 ASP A 316 ILE A 327 1 O ILE A 319 N LYS A 281 SHEET 5 A 6 TRP A 301 ASP A 311 -1 N LYS A 303 O ASN A 325 SHEET 6 A 6 GLU A 243 GLU A 259 -1 N VAL A 248 O VAL A 304 SHEET 1 B 3 ILE A 375 VAL A 377 0 SHEET 2 B 3 VAL A 400 VAL A 409 1 O ILE A 401 N VAL A 377 SHEET 3 B 3 ILE A 652 PRO A 653 1 O ILE A 652 N ASN A 407 SHEET 1 C 4 ILE A 375 VAL A 377 0 SHEET 2 C 4 VAL A 400 VAL A 409 1 O ILE A 401 N VAL A 377 SHEET 3 C 4 PHE A 619 ALA A 625 -1 O LEU A 623 N LEU A 404 SHEET 4 C 4 LEU A 664 GLY A 667 -1 O GLY A 667 N THR A 622 SHEET 1 D 2 LEU A 697 VAL A 699 0 SHEET 2 D 2 VAL A 738 ALA A 740 1 O VAL A 739 N LEU A 697 SHEET 1 E 7 GLY A 891 SER A 892 0 SHEET 2 E 7 ILE A 974 SER A 979 -1 O ASN A 977 N GLY A 891 SHEET 3 E 7 LYS A1096 HIS A1102 1 O ASP A1098 N LEU A 976 SHEET 4 E 7 LYS A1044 VAL A1056 -1 N ILE A1054 O LEU A1097 SHEET 5 E 7 VAL A 999 THR A1007 -1 N GLY A1006 O ARG A1045 SHEET 6 E 7 THR A1082 ASP A1086 1 O THR A1083 N ARG A1001 SHEET 7 E 7 ILE A1069 GLN A1070 -1 N GLN A1070 O THR A1082 SHEET 1 F 3 SER A 925 PHE A 927 0 SHEET 2 F 3 HIS A 916 VAL A 918 -1 N TYR A 917 O GLU A 926 SHEET 3 F 3 LYS A 952 ASP A 954 -1 O LYS A 952 N VAL A 918 SHEET 1 G 3 SER A1358 PHE A1359 0 SHEET 2 G 3 SER A1378 ILE A1380 1 O LEU A1379 N SER A1358 SHEET 3 G 3 VAL A1373 ASP A1375 -1 N VAL A1373 O ILE A1380 LINK ZN ZN A 4 SG CYS A 919 1555 1555 2.62 LINK ZN ZN A 4 SG CYS A 922 1555 1555 2.26 LINK ZN ZN A 4 SG CYS A 944 1555 1555 2.15 LINK ZN ZN A 4 SG CYS A 947 1555 1555 2.53 LINK MG MG A 5 OD2 ASP A 973 1555 1555 2.19 LINK MG MG A 5 OD2 ASP A 975 1555 1555 2.04 LINK MG MG A 5 O2A DGT A1456 1555 1555 1.86 LINK MG MG A 5 O2G DGT A1456 1555 1555 2.18 LINK MG MG A 5 O1B DGT A1456 1555 1555 1.97 LINK MG MG A 5 O HOH A1457 1555 1555 2.27 LINK MG MG A 6 O HOH A 92 1555 1555 2.30 LINK MG MG A 6 OE1 GLU A 405 1555 1555 2.18 LINK MG MG A 7 O HOH A 92 1555 1555 2.49 LINK MG MG A 7 NE2 HIS A 346 1555 1555 2.32 LINK MG MG A 7 NE2 HIS A 348 1555 1555 2.48 LINK MG MG A 7 OE1 GLU A 405 1555 1555 2.48 LINK MG MG A 7 OD1 ASN A 743 1555 1555 2.31 CISPEP 1 ASP A 847 PRO A 848 0 3.17 SITE 1 AC1 4 HOH A 83 SER A 789 LYS A 882 ARG A 985 SITE 1 AC2 5 LYS A 756 HIS A 760 ASN A 769 TYR A1020 SITE 2 AC2 5 HIS A1024 SITE 1 AC3 2 LYS A 636 HIS A 660 SITE 1 AC4 4 CYS A 919 CYS A 922 CYS A 944 CYS A 947 SITE 1 AC5 4 ASP A 973 ASP A 975 DGT A1456 HOH A1457 SITE 1 AC6 5 MG A 7 HOH A 92 GLU A 405 HIS A 620 SITE 2 AC6 5 CYS A 670 SITE 1 AC7 6 MG A 6 HOH A 92 HIS A 346 HIS A 348 SITE 2 AC7 6 GLU A 405 ASN A 743 SITE 1 AC8 24 MG A 5 HOH A 10 HOH A 11 HOH A 12 SITE 2 AC8 24 HOH A 68 HOH A 99 ARG A 893 GLY A 894 SITE 3 AC8 24 SER A 895 LYS A 970 PRO A 972 ASP A 973 SITE 4 AC8 24 ASP A 975 HIS A1186 ARG A1213 ARG A1238 SITE 5 AC8 24 TYR A1269 PHE A1271 PRO A1272 HIS A1275 SITE 6 AC8 24 HOH A1457 DC P 17 DC T 5 DG T 6 CRYST1 116.174 140.793 184.524 90.00 90.00 90.00 C 2 2 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008608 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007103 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005419 0.00000