PDB Short entry for 6FBG HEADER DNA BINDING PROTEIN 19-DEC-17 6FBG TITLE KLENTAQ DNA POLYMERASE PROCESSING A MODIFIED PRIMER - BEARING THE TITLE 2 MODIFICATION UPSTREAM AT THE FIFTH PRIMER NUCLEOTIDE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TAQ POLYMERASE 1; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*AP*CP*CP*AP*CP*AP*(OH3)P*CP*GP*GP*C)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*AP*AP*AP*CP*GP*CP*CP*GP*GP*TP*GP*TP*GP*GP*TP*C)- COMPND 13 3'); COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 GENE: POLA, POL1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS DNA POLYMERASE, MODIFIED NUCLEOTIDES, KLENTAQ, KLENTAQ DNA KEYWDS 2 POLYMERASE, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.M.KROPP,K.DIEDERICHS,A.MARX REVDAT 3 14-AUG-19 6FBG 1 COMPND REMARK REVDAT 2 10-OCT-18 6FBG 1 COMPND JRNL REVDAT 1 26-SEP-18 6FBG 0 JRNL AUTH H.M.KROPP,S.L.DURR,C.PETER,K.DIEDERICHS,A.MARX JRNL TITL SNAPSHOTS OF A MODIFIED NUCLEOTIDE MOVING THROUGH THE JRNL TITL 2 CONFINES OF A DNA POLYMERASE. JRNL REF PROC. NATL. ACAD. SCI. V. 115 9992 2018 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 30224478 JRNL DOI 10.1073/PNAS.1811518115 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12RC1_2815: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.160 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 132682 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 6727 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 47.3414 - 5.2871 1.00 4194 240 0.1798 0.1958 REMARK 3 2 5.2871 - 4.1974 1.00 4217 211 0.1535 0.1907 REMARK 3 3 4.1974 - 3.6670 1.00 4184 258 0.1543 0.1616 REMARK 3 4 3.6670 - 3.3318 1.00 4163 235 0.1570 0.1645 REMARK 3 5 3.3318 - 3.0931 1.00 4191 248 0.1708 0.1920 REMARK 3 6 3.0931 - 2.9107 1.00 4209 215 0.1782 0.2036 REMARK 3 7 2.9107 - 2.7650 1.00 4226 231 0.1777 0.2054 REMARK 3 8 2.7650 - 2.6446 1.00 4201 219 0.1851 0.2179 REMARK 3 9 2.6446 - 2.5428 1.00 4166 228 0.1833 0.2166 REMARK 3 10 2.5428 - 2.4551 1.00 4166 250 0.1968 0.2657 REMARK 3 11 2.4551 - 2.3783 1.00 4238 199 0.1953 0.2254 REMARK 3 12 2.3783 - 2.3103 1.00 4263 187 0.2017 0.2289 REMARK 3 13 2.3103 - 2.2495 1.00 4201 235 0.2109 0.2528 REMARK 3 14 2.2495 - 2.1946 1.00 4203 183 0.2118 0.2533 REMARK 3 15 2.1946 - 2.1448 1.00 4224 209 0.2146 0.2466 REMARK 3 16 2.1448 - 2.0991 1.00 4220 208 0.2356 0.2567 REMARK 3 17 2.0991 - 2.0571 1.00 4180 215 0.2495 0.2615 REMARK 3 18 2.0571 - 2.0183 1.00 4218 224 0.2659 0.2904 REMARK 3 19 2.0183 - 1.9823 1.00 4185 250 0.2785 0.2999 REMARK 3 20 1.9823 - 1.9487 1.00 4213 244 0.2917 0.3165 REMARK 3 21 1.9487 - 1.9172 1.00 4169 202 0.2913 0.3099 REMARK 3 22 1.9172 - 1.8877 1.00 4249 220 0.3063 0.3091 REMARK 3 23 1.8877 - 1.8600 1.00 4173 241 0.3211 0.3478 REMARK 3 24 1.8600 - 1.8338 1.00 4220 248 0.3344 0.3652 REMARK 3 25 1.8338 - 1.8090 1.00 4165 232 0.3396 0.3392 REMARK 3 26 1.8090 - 1.7855 1.00 4206 197 0.3526 0.3421 REMARK 3 27 1.7855 - 1.7632 1.00 4148 228 0.3621 0.3889 REMARK 3 28 1.7632 - 1.7419 1.00 4201 222 0.3695 0.3523 REMARK 3 29 1.7419 - 1.7217 1.00 4188 211 0.3875 0.4048 REMARK 3 30 1.7217 - 1.7023 0.99 4174 237 0.3917 0.4329 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 5040 REMARK 3 ANGLE : 0.583 6933 REMARK 3 CHIRALITY : 0.040 766 REMARK 3 PLANARITY : 0.003 839 REMARK 3 DIHEDRAL : 15.896 2950 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 294 THROUGH 452 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.4294 -41.2218 -18.1490 REMARK 3 T TENSOR REMARK 3 T11: 0.2954 T22: 0.3319 REMARK 3 T33: 0.4601 T12: -0.0686 REMARK 3 T13: 0.0906 T23: -0.0843 REMARK 3 L TENSOR REMARK 3 L11: 0.7726 L22: 2.5363 REMARK 3 L33: 1.5342 L12: -0.1210 REMARK 3 L13: -0.3639 L23: -0.2290 REMARK 3 S TENSOR REMARK 3 S11: -0.0723 S12: 0.0487 S13: -0.4094 REMARK 3 S21: -0.1814 S22: -0.0135 S23: -0.4474 REMARK 3 S31: 0.2221 S32: 0.1229 S33: 0.0772 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 453 THROUGH 603 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.1000 -11.1890 1.7224 REMARK 3 T TENSOR REMARK 3 T11: 0.3247 T22: 0.2095 REMARK 3 T33: 0.2820 T12: -0.0049 REMARK 3 T13: 0.0471 T23: -0.0035 REMARK 3 L TENSOR REMARK 3 L11: 1.5588 L22: 1.5089 REMARK 3 L33: 2.4620 L12: 0.8366 REMARK 3 L13: -0.4433 L23: -0.1069 REMARK 3 S TENSOR REMARK 3 S11: 0.1679 S12: -0.1378 S13: 0.2065 REMARK 3 S21: 0.1517 S22: -0.0398 S23: 0.0594 REMARK 3 S31: -0.6542 S32: 0.0664 S33: -0.1095 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 604 THROUGH 685 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.1507 -13.6788 -8.1192 REMARK 3 T TENSOR REMARK 3 T11: 0.4520 T22: 0.5525 REMARK 3 T33: 0.2789 T12: 0.2145 REMARK 3 T13: 0.0128 T23: 0.0603 REMARK 3 L TENSOR REMARK 3 L11: 1.7802 L22: 1.4593 REMARK 3 L33: 2.3428 L12: 0.3010 REMARK 3 L13: -0.6395 L23: 0.0644 REMARK 3 S TENSOR REMARK 3 S11: -0.0303 S12: -0.1056 S13: 0.2256 REMARK 3 S21: 0.1315 S22: 0.1726 S23: 0.3053 REMARK 3 S31: -0.7608 S32: -0.7333 S33: -0.1025 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 686 THROUGH 831 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.5484 -25.2374 -12.9245 REMARK 3 T TENSOR REMARK 3 T11: 0.2174 T22: 0.3740 REMARK 3 T33: 0.2340 T12: 0.0254 REMARK 3 T13: 0.0132 T23: 0.0130 REMARK 3 L TENSOR REMARK 3 L11: 1.2319 L22: 1.0955 REMARK 3 L33: 2.6431 L12: 0.5839 REMARK 3 L13: -0.2045 L23: -0.6289 REMARK 3 S TENSOR REMARK 3 S11: -0.0362 S12: 0.1420 S13: -0.0141 REMARK 3 S21: -0.0457 S22: 0.1844 S23: 0.1072 REMARK 3 S31: -0.2596 S32: -0.5648 S33: -0.1219 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 101 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.8718 -23.1688 4.1864 REMARK 3 T TENSOR REMARK 3 T11: 0.2908 T22: 0.3401 REMARK 3 T33: 0.3683 T12: -0.0053 REMARK 3 T13: 0.0559 T23: 0.0220 REMARK 3 L TENSOR REMARK 3 L11: 0.8838 L22: 2.3188 REMARK 3 L33: 5.3262 L12: 0.4664 REMARK 3 L13: 1.6716 L23: -1.1592 REMARK 3 S TENSOR REMARK 3 S11: 0.0646 S12: 0.2561 S13: -0.2446 REMARK 3 S21: 0.0445 S22: -0.2595 S23: -0.2462 REMARK 3 S31: 0.0637 S32: 0.3378 S33: 0.1504 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 201 THROUGH 205 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.8221 -21.0516 7.3503 REMARK 3 T TENSOR REMARK 3 T11: 0.5592 T22: 0.8587 REMARK 3 T33: 0.4220 T12: 0.1314 REMARK 3 T13: 0.0044 T23: -0.0470 REMARK 3 L TENSOR REMARK 3 L11: 5.3767 L22: 8.2506 REMARK 3 L33: 4.2656 L12: 5.2357 REMARK 3 L13: 4.7668 L23: 4.2506 REMARK 3 S TENSOR REMARK 3 S11: -0.2064 S12: -1.6170 S13: 0.9586 REMARK 3 S21: 1.5070 S22: -0.3081 S23: 0.4126 REMARK 3 S31: 0.3429 S32: -0.5296 S33: 0.4604 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 206 THROUGH 216 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.9317 -24.1547 6.0506 REMARK 3 T TENSOR REMARK 3 T11: 0.2993 T22: 0.3014 REMARK 3 T33: 0.3316 T12: 0.0394 REMARK 3 T13: -0.0209 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 3.5675 L22: 3.5821 REMARK 3 L33: 1.7182 L12: 0.6269 REMARK 3 L13: -2.0994 L23: 0.7821 REMARK 3 S TENSOR REMARK 3 S11: -0.1763 S12: -0.2480 S13: -0.1761 REMARK 3 S21: 0.3872 S22: 0.2986 S23: -0.5540 REMARK 3 S31: -0.0045 S32: 0.5841 S33: -0.1686 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6FBG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200007860. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 132688 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.702 REMARK 200 RESOLUTION RANGE LOW (A) : 47.323 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.170 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.3900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.580 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15 % PEG 4000, 0.1 M HEPES, 20 MM REMARK 280 MANGANESE(II) CHLORIDE, 0.1 M SODIUM ACETATE, PH 7.0, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.24100 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 60.48200 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 60.48200 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.24100 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: 7050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 292 REMARK 465 ALA A 293 REMARK 465 GLU A 832 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 LYS A 340 CG CD CE NZ REMARK 470 LYS A 346 CG CD CE NZ REMARK 470 LEU A 365 CG CD1 CD2 REMARK 470 ARG A 392 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 400 CG CD OE1 OE2 REMARK 470 GLU A 421 CG CD OE1 OE2 REMARK 470 GLU A 424 CG CD OE1 OE2 REMARK 470 GLU A 462 CG CD OE1 OE2 REMARK 470 ARG A 556 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 630 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 649 CG1 CG2 REMARK 470 LEU A 657 CG CD1 CD2 REMARK 470 GLU A 694 CG CD OE1 OE2 REMARK 470 GLN A 698 CG CD OE1 NE2 REMARK 470 GLU A 708 CG CD OE1 OE2 REMARK 470 LYS A 709 CG CD CE NZ REMARK 470 GLU A 713 CG CD OE1 OE2 REMARK 470 ARG A 795 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 801 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 831 CG CD CE NZ 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 O HOH B 202 O HOH B 225 2.05 REMARK 500 O HOH A 1171 O HOH C 425 2.07 REMARK 500 O HOH A 1171 O HOH A 1182 2.08 REMARK 500 O HOH B 226 O HOH C 424 2.08 REMARK 500 O HOH A 1141 O HOH A 1188 2.09 REMARK 500 O HOH A 1144 O HOH A 1181 2.09 REMARK 500 O HOH A 1162 O HOH C 433 2.10 REMARK 500 O HOH B 226 O HOH C 409 2.14 REMARK 500 O HOH A 1054 O HOH A 1185 2.15 REMARK 500 O HOH A 1194 O HOH C 425 2.18 REMARK 500 O HOH A 1161 O HOH A 1196 2.19 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 D4B B 108 O3' - P - OP1 ANGL. DEV. = 16.4 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 2.1 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 ARG A 328 145.36 -173.02 REMARK 500 ASP A 381 106.65 -161.45 REMARK 500 THR A 399 -167.91 -106.16 REMARK 500 VAL A 433 -67.82 -126.70 REMARK 500 TYR A 545 -56.67 -127.83 REMARK 500 VAL A 586 -16.56 -155.81 REMARK 500 HIS A 784 -60.93 76.35 REMARK 500 TYR A 811 93.35 -162.51 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 MN A 901 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD1 REMARK 620 2 TYR A 611 O 77.9 REMARK 620 3 ASP A 785 OD2 91.6 89.3 REMARK 620 4 XG4 A 907 O1A 98.5 173.2 85.1 REMARK 620 5 XG4 A 907 O1B 171.7 98.6 95.9 85.7 REMARK 620 6 XG4 A 907 O3G 85.6 90.1 177.2 95.3 86.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 902 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD2 REMARK 620 2 ASP A 785 OD1 97.1 REMARK 620 3 DC B 112 O3' 166.7 75.8 REMARK 620 4 XG4 A 907 O1A 104.1 93.3 87.6 REMARK 620 5 HOH A1023 O 90.2 99.0 80.1 159.9 REMARK 620 6 HOH A1108 O 94.1 168.8 93.3 83.7 81.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 906 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue XG4 A 907 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 302 DBREF 6FBG A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 6FBG B 101 112 PDB 6FBG 6FBG 101 112 DBREF 6FBG C 201 216 PDB 6FBG 6FBG 201 216 SEQADV 6FBG MET A 292 UNP P19821 INITIATING METHIONINE SEQRES 1 A 541 MET ALA LEU GLU GLU ALA PRO TRP PRO PRO PRO GLU GLY SEQRES 2 A 541 ALA PHE VAL GLY PHE VAL LEU SER ARG LYS GLU PRO MET SEQRES 3 A 541 TRP ALA ASP LEU LEU ALA LEU ALA ALA ALA ARG GLY GLY SEQRES 4 A 541 ARG VAL HIS ARG ALA PRO GLU PRO TYR LYS ALA LEU ARG SEQRES 5 A 541 ASP LEU LYS GLU ALA ARG GLY LEU LEU ALA LYS ASP LEU SEQRES 6 A 541 SER VAL LEU ALA LEU ARG GLU GLY LEU GLY LEU PRO PRO SEQRES 7 A 541 GLY ASP ASP PRO MET LEU LEU ALA TYR LEU LEU ASP PRO SEQRES 8 A 541 SER ASN THR THR PRO GLU GLY VAL ALA ARG ARG TYR GLY SEQRES 9 A 541 GLY GLU TRP THR GLU GLU ALA GLY GLU ARG ALA ALA LEU SEQRES 10 A 541 SER GLU ARG LEU PHE ALA ASN LEU TRP GLY ARG LEU GLU SEQRES 11 A 541 GLY GLU GLU ARG LEU LEU TRP LEU TYR ARG GLU VAL GLU SEQRES 12 A 541 ARG PRO LEU SER ALA VAL LEU ALA HIS MET GLU ALA THR SEQRES 13 A 541 GLY VAL ARG LEU ASP VAL ALA TYR LEU ARG ALA LEU SER SEQRES 14 A 541 LEU GLU VAL ALA GLU GLU ILE ALA ARG LEU GLU ALA GLU SEQRES 15 A 541 VAL PHE ARG LEU ALA GLY HIS PRO PHE ASN LEU ASN SER SEQRES 16 A 541 ARG ASP GLN LEU GLU ARG VAL LEU PHE ASP GLU LEU GLY SEQRES 17 A 541 LEU PRO ALA ILE GLY LYS THR GLU LYS THR GLY LYS ARG SEQRES 18 A 541 SER THR SER ALA ALA VAL LEU GLU ALA LEU ARG GLU ALA SEQRES 19 A 541 HIS PRO ILE VAL GLU LYS ILE LEU GLN TYR ARG GLU LEU SEQRES 20 A 541 THR LYS LEU LYS SER THR TYR ILE ASP PRO LEU PRO ASP SEQRES 21 A 541 LEU ILE HIS PRO ARG THR GLY ARG LEU HIS THR ARG PHE SEQRES 22 A 541 ASN GLN THR ALA THR ALA THR GLY ARG LEU SER SER SER SEQRES 23 A 541 ASP PRO ASN LEU GLN ASN ILE PRO VAL ARG THR PRO LEU SEQRES 24 A 541 GLY GLN ARG ILE ARG ARG ALA PHE ILE ALA GLU GLU GLY SEQRES 25 A 541 TRP LEU LEU VAL ALA LEU ASP TYR SER GLN ILE GLU LEU SEQRES 26 A 541 ARG VAL LEU ALA HIS LEU SER GLY ASP GLU ASN LEU ILE SEQRES 27 A 541 ARG VAL PHE GLN GLU GLY ARG ASP ILE HIS THR GLU THR SEQRES 28 A 541 ALA SER TRP MET PHE GLY VAL PRO ARG GLU ALA VAL ASP SEQRES 29 A 541 PRO LEU MET ARG ARG ALA ALA LYS THR ILE ASN PHE GLY SEQRES 30 A 541 VAL LEU TYR GLY MET SER ALA HIS ARG LEU SER GLN GLU SEQRES 31 A 541 LEU ALA ILE PRO TYR GLU GLU ALA GLN ALA PHE ILE GLU SEQRES 32 A 541 ARG TYR PHE GLN SER PHE PRO LYS VAL ARG ALA TRP ILE SEQRES 33 A 541 GLU LYS THR LEU GLU GLU GLY ARG ARG ARG GLY TYR VAL SEQRES 34 A 541 GLU THR LEU PHE GLY ARG ARG ARG TYR VAL PRO ASP LEU SEQRES 35 A 541 GLU ALA ARG VAL LYS SER VAL ARG GLU ALA ALA GLU ARG SEQRES 36 A 541 MET ALA PHE ASN MET PRO VAL GLN GLY THR ALA ALA ASP SEQRES 37 A 541 LEU MET LYS LEU ALA MET VAL LYS LEU PHE PRO ARG LEU SEQRES 38 A 541 GLU GLU MET GLY ALA ARG MET LEU LEU GLN VAL HIS ASP SEQRES 39 A 541 GLU LEU VAL LEU GLU ALA PRO LYS GLU ARG ALA GLU ALA SEQRES 40 A 541 VAL ALA ARG LEU ALA LYS GLU VAL MET GLU GLY VAL TYR SEQRES 41 A 541 PRO LEU ALA VAL PRO LEU GLU VAL GLU VAL GLY ILE GLY SEQRES 42 A 541 GLU ASP TRP LEU SER ALA LYS GLU SEQRES 1 B 12 DG DA DC DC DA DC DA D4B DC DG DG DC SEQRES 1 C 16 DA DA DA DC DG DC DC DG DG DT DG DT DG SEQRES 2 C 16 DG DT DC HET D4B B 108 44 HET MN A 901 1 HET MN A 902 1 HET EDO A 903 10 HET EDO A 904 10 HET EDO A 905 10 HET EDO A 906 10 HET XG4 A 907 44 HET EDO C 301 20 HET EDO C 302 10 HETNAM D4B [(2~{R},3~{S},5~{R})-5-[4-AZANYL-5-[2-(4- HETNAM 2 D4B ETHYNYLPHENYL)ETHYNYL]-2-OXIDANYLIDENE-PYRIMIDIN-1- HETNAM 3 D4B YL]-3-OXIDANYL-OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM EDO 1,2-ETHANEDIOL HETNAM XG4 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 XG4 PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 D4B C19 H18 N3 O7 P FORMUL 4 MN 2(MN 2+) FORMUL 6 EDO 6(C2 H6 O2) FORMUL 10 XG4 C10 H17 N6 O12 P3 FORMUL 13 HOH *266(H2 O) HELIX 1 AA1 GLU A 337 LEU A 342 1 6 HELIX 2 AA2 ARG A 343 LEU A 345 5 3 HELIX 3 AA3 LEU A 352 GLU A 363 1 12 HELIX 4 AA4 ASP A 372 ASP A 381 1 10 HELIX 5 AA5 THR A 386 GLY A 395 1 10 HELIX 6 AA6 GLU A 401 LEU A 420 1 20 HELIX 7 AA7 GLU A 423 VAL A 433 1 11 HELIX 8 AA8 VAL A 433 GLY A 448 1 16 HELIX 9 AA9 ASP A 452 GLY A 479 1 28 HELIX 10 AB1 SER A 486 ASP A 496 1 11 HELIX 11 AB2 SER A 515 LEU A 522 1 8 HELIX 12 AB3 HIS A 526 TYR A 545 1 20 HELIX 13 AB4 PRO A 548 ILE A 553 5 6 HELIX 14 AB5 THR A 588 ARG A 596 1 9 HELIX 15 AB6 GLN A 613 GLY A 624 1 12 HELIX 16 AB7 ASP A 625 GLU A 634 1 10 HELIX 17 AB8 ASP A 637 GLY A 648 1 12 HELIX 18 AB9 PRO A 650 VAL A 654 5 5 HELIX 19 AC1 ASP A 655 TYR A 671 1 17 HELIX 20 AC2 SER A 674 ALA A 683 1 10 HELIX 21 AC3 PRO A 685 PHE A 700 1 16 HELIX 22 AC4 PRO A 701 GLY A 718 1 18 HELIX 23 AC5 PRO A 731 ALA A 735 5 5 HELIX 24 AC6 VAL A 737 GLY A 776 1 40 HELIX 25 AC7 ARG A 795 GLY A 809 1 15 SHEET 1 AA1 4 GLU A 295 ALA A 297 0 SHEET 2 AA1 4 ARG A 331 ARG A 334 1 O VAL A 332 N ALA A 297 SHEET 3 AA1 4 LEU A 321 ARG A 328 -1 N ALA A 326 O HIS A 333 SHEET 4 AA1 4 PHE A 306 LEU A 311 -1 N GLY A 308 O ALA A 325 SHEET 1 AA2 2 ARG A 450 LEU A 451 0 SHEET 2 AA2 2 PHE A 598 ILE A 599 -1 O ILE A 599 N ARG A 450 SHEET 1 AA3 2 ARG A 563 ASN A 565 0 SHEET 2 AA3 2 SER A 575 SER A 577 -1 O SER A 577 N ARG A 563 SHEET 1 AA4 4 ARG A 778 GLN A 782 0 SHEET 2 AA4 4 GLU A 786 PRO A 792 -1 O GLU A 790 N ARG A 778 SHEET 3 AA4 4 TRP A 604 TYR A 611 -1 N VAL A 607 O LEU A 789 SHEET 4 AA4 4 VAL A 819 GLY A 824 -1 O GLY A 824 N LEU A 606 SHEET 1 AA5 2 TYR A 719 GLU A 721 0 SHEET 2 AA5 2 ARG A 727 TYR A 729 -1 O ARG A 728 N VAL A 720 LINK OD1 ASP A 610 MN MN A 901 1555 1555 2.13 LINK OD2 ASP A 610 MN MN A 902 1555 1555 2.15 LINK O TYR A 611 MN MN A 901 1555 1555 2.11 LINK OD1 ASP A 785 MN MN A 902 1555 1555 2.13 LINK OD2 ASP A 785 MN MN A 901 1555 1555 2.14 LINK O3' DA B 107 P D4B B 108 1555 1555 1.59 LINK O3' D4B B 108 P DC B 109 1555 1555 1.60 LINK O3' DC B 112 MN MN A 902 1555 1555 2.24 LINK MN MN A 901 O1A XG4 A 907 1555 1555 2.37 LINK MN MN A 901 O1B XG4 A 907 1555 1555 2.25 LINK MN MN A 901 O3G XG4 A 907 1555 1555 2.11 LINK MN MN A 902 O1A XG4 A 907 1555 1555 2.23 LINK MN MN A 902 O HOH A1023 1555 1555 2.17 LINK MN MN A 902 O HOH A1108 1555 1555 2.23 CISPEP 1 TRP A 299 PRO A 300 0 1.58 CISPEP 2 ASP A 578 PRO A 579 0 -0.29 SITE 1 AC1 5 ASP A 610 TYR A 611 ASP A 785 MN A 902 SITE 2 AC1 5 XG4 A 907 SITE 1 AC2 7 ASP A 610 ASP A 785 MN A 901 XG4 A 907 SITE 2 AC2 7 HOH A1023 HOH A1108 DC B 112 SITE 1 AC3 3 ARG A 450 GLU A 465 GLU A 602 SITE 1 AC4 6 PHE A 309 LEU A 311 LEU A 352 ARG A 405 SITE 2 AC4 6 HOH A1019 HOH A1074 SITE 1 AC5 4 LYS A 354 ASP A 355 HOH A1010 HOH A1022 SITE 1 AC6 5 HIS A 621 ARG A 771 GLU A 774 MET A 775 SITE 2 AC6 5 HOH A1088 SITE 1 AC7 25 ARG A 573 ASP A 610 TYR A 611 SER A 612 SITE 2 AC7 25 GLN A 613 ILE A 614 GLU A 615 HIS A 639 SITE 3 AC7 25 ARG A 659 LYS A 663 PHE A 667 TYR A 671 SITE 4 AC7 25 ASP A 785 MN A 901 MN A 902 HOH A1049 SITE 5 AC7 25 HOH A1054 HOH A1084 HOH A1092 HOH A1108 SITE 6 AC7 25 HOH A1155 DC B 112 HOH B 207 DC C 204 SITE 7 AC7 25 DG C 205 SITE 1 AC8 2 DG C 213 DG C 214 SITE 1 AC9 2 DC C 206 DC C 207 CRYST1 109.288 109.288 90.723 90.00 90.00 120.00 P 31 2 1 6 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 0.009150 0.005283 0.000000 0.00000 SCALE2 0.000000 0.010566 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011023 0.00000