PDB Short entry for 4XA5 HEADER TRANSFERASE/DNA 12-DEC-14 4XA5 TITLE CRYSTAL STRUCTURE OF THE PRE-CATALYTIC TERNARY COMPLEX OF DNA TITLE 2 POLYMERASE LAMBDA WITH A TEMPLATING A AND AN INCOMING 8-OXO-DGTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE LAMBDA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POL LAMBDA,DNA POLYMERASE BETA-2,POL BETA2,DNA POLYMERASE COMPND 5 KAPPA; COMPND 6 EC: 2.7.7.7,4.2.99.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DOWNSTREAM PRIMER DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 10 CHAIN: D; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: PRIMER DNA (5'-D(*CP*AP*GP*TP*AP*(DOC))-3'); COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: TEMPLATE DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3'); COMPND 18 CHAIN: T; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630; SOURCE 17 MOL_ID: 4; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 20 ORGANISM_TAXID: 32630 KEYWDS DNA POLYMERASE LAMBDA, PROTEIN-DNA COMPLEX, HELIX-HAIRPIN-HELIX, KEYWDS 2 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.J.BURAK,K.E.GUJA,M.GARCIA-DIAZ REVDAT 1 10-FEB-16 4XA5 0 JRNL AUTH M.J.BURAK,K.E.GUJA,M.GARCIA-DIAZ JRNL TITL NUCLEOTIDE BINDING INTERACTIONS MODULATE DNTP SELECTIVITY JRNL TITL 2 AND FACILITATE 8-OXO-DGTP INCORPORATION BY DNA POLYMERASE JRNL TITL 3 LAMBDA. JRNL REF NUCLEIC ACIDS RES. V. 43 8089 2015 JRNL REFN ESSN 1362-4962 JRNL PMID 26220180 JRNL DOI 10.1093/NAR/GKV760 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 38044 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1971 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2791 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 137 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2384 REMARK 3 NUCLEIC ACID ATOMS : 425 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 247 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.43000 REMARK 3 B33 (A**2) : -0.42000 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): 0.134 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.126 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.097 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.925 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2964 ; 0.018 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 2548 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4102 ; 1.985 ; 1.849 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5845 ; 1.262 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 314 ; 7.081 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 103 ;34.942 ;22.816 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 388 ;13.874 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;17.952 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 439 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3066 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 688 ; 0.002 ; 0.020 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): 1259 ; 2.179 ; 2.353 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1255 ; 2.144 ; 2.343 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1567 ; 3.050 ; 3.499 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1568 ; 3.049 ; 3.501 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1705 ; 2.612 ; 2.529 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1705 ; 2.607 ; 2.529 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2535 ; 3.685 ; 3.724 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3756 ; 7.114 ;21.462 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3631 ; 6.990 ;20.817 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 : 3 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 252 A 575 REMARK 3 ORIGIN FOR THE GROUP (A): -13.3172 10.7258 -15.5205 REMARK 3 T TENSOR REMARK 3 T11: 0.0629 T22: 0.0401 REMARK 3 T33: 0.0677 T12: -0.0225 REMARK 3 T13: 0.0185 T23: -0.0097 REMARK 3 L TENSOR REMARK 3 L11: 1.6923 L22: 2.3945 REMARK 3 L33: 1.6546 L12: -0.1643 REMARK 3 L13: 0.8666 L23: 0.9568 REMARK 3 S TENSOR REMARK 3 S11: 0.0469 S12: 0.1977 S13: -0.1237 REMARK 3 S21: -0.3306 S22: 0.1491 S23: -0.0315 REMARK 3 S31: -0.0685 S32: 0.1132 S33: -0.1959 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 : P 1 P 6 REMARK 3 ORIGIN FOR THE GROUP (A): -25.5864 14.6074 -8.7273 REMARK 3 T TENSOR REMARK 3 T11: 0.1119 T22: 0.0414 REMARK 3 T33: 0.1153 T12: -0.0495 REMARK 3 T13: -0.0301 T23: 0.0469 REMARK 3 L TENSOR REMARK 3 L11: 1.0099 L22: 3.0264 REMARK 3 L33: 4.3681 L12: 0.6029 REMARK 3 L13: 1.9979 L23: 0.2121 REMARK 3 S TENSOR REMARK 3 S11: -0.0610 S12: -0.0155 S13: 0.0503 REMARK 3 S21: -0.4683 S22: 0.0559 S23: 0.0192 REMARK 3 S31: 0.1269 S32: -0.1062 S33: 0.0051 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 : T 1 T 11 REMARK 3 ORIGIN FOR THE GROUP (A): -27.2803 15.2819 -17.4205 REMARK 3 T TENSOR REMARK 3 T11: 0.2715 T22: 0.1510 REMARK 3 T33: 0.2009 T12: -0.0681 REMARK 3 T13: -0.1904 T23: 0.0628 REMARK 3 L TENSOR REMARK 3 L11: 1.6300 L22: 0.7155 REMARK 3 L33: 1.0095 L12: 0.1694 REMARK 3 L13: -0.1711 L23: 0.7871 REMARK 3 S TENSOR REMARK 3 S11: -0.2469 S12: 0.4904 S13: 0.2569 REMARK 3 S21: -0.2236 S22: -0.0017 S23: 0.3143 REMARK 3 S31: -0.1030 S32: -0.1100 S33: 0.2487 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 4XA5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000205299. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00003 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40080 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 46.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE TRIHYDRATE PH REMARK 280 7.4 AND 1.9 M SODIUM ACETATE TRIHYDRATE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 27.98350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.80650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.17000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.80650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.98350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.17000 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, 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 ASN A 251 REMARK 465 VAL A 537 REMARK 465 ARG A 538 REMARK 465 ASN A 539 REMARK 465 THR A 540 REMARK 465 HIS A 541 REMARK 465 GLY A 542 REMARK 465 CYS A 543 REMARK 465 LYS A 544 REMARK 465 VAL A 545 REMARK 465 GLY A 546 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 HIS A 252 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A 256 CG1 CG2 CD1 REMARK 470 GLU A 258 CG CD OE1 OE2 REMARK 470 LYS A 259 CD CE NZ REMARK 470 LYS A 265 CD CE NZ REMARK 470 LYS A 281 CG CD CE NZ REMARK 470 LEU A 286 CD1 CD2 REMARK 470 LYS A 287 CE NZ REMARK 470 SER A 295 OG REMARK 470 GLN A 297 CG CD OE1 NE2 REMARK 470 LYS A 307 CG CD CE NZ REMARK 470 ILE A 314 CG1 CG2 CD1 REMARK 470 GLU A 318 CG CD OE1 OE2 REMARK 470 SER A 319 OG REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 324 CD CE NZ REMARK 470 GLU A 390 CG CD OE1 OE2 REMARK 470 GLN A 397 CD OE1 NE2 REMARK 470 LYS A 401 CG CD CE NZ REMARK 470 LYS A 422 CE NZ REMARK 470 ARG A 438 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 441 CG CD NE CZ NH1 NH2 REMARK 470 SER A 445 OG REMARK 470 ARG A 446 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 449 CG OD1 OD2 REMARK 470 GLN A 453 CD OE1 NE2 REMARK 470 GLU A 466 CG CD OE1 OE2 REMARK 470 GLN A 469 CG CD OE1 NE2 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 OE1 GLN A 404 O HOH A 701 1.88 REMARK 500 O HOH A 851 O HOH T 131 2.07 REMARK 500 OD1 ASP A 429 O HOH A 746 2.09 REMARK 500 OP2 DG D 1 O HOH D 104 2.12 REMARK 500 NH1 ARG A 308 OP3 DG D 1 2.16 REMARK 500 O HOH A 752 O HOH A 833 2.17 REMARK 500 OD2 ASP A 427 O HOH A 746 2.18 REMARK 500 OP2 DA T 8 O HOH T 132 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 703 O HOH T 102 4555 2.18 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 DG D 1 P DG D 1 OP3 -0.126 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 DC T 1 C5' - C4' - O4' ANGL. DEV. = 7.2 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 358 -8.90 -140.99 REMARK 500 CYS A 415 -137.92 -108.23 REMARK 500 ASP A 427 -169.20 -163.61 REMARK 500 ARG A 438 -42.30 -135.54 REMARK 500 SER A 463 97.01 -161.49 REMARK 500 ASP A 574 67.29 -101.97 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 MG A 603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 339 O REMARK 620 2 ILE A 341 O 97.3 REMARK 620 3 ALA A 344 O 90.8 85.6 REMARK 620 4 DA P 5 OP1 161.7 101.1 90.9 REMARK 620 5 HOH A 760 O 89.1 97.1 177.2 88.4 REMARK 620 6 HOH P 110 O 76.6 171.7 88.8 85.2 88.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD1 REMARK 620 2 ASP A 429 OD2 96.0 REMARK 620 3 8DG A 601 O2G 88.3 174.8 REMARK 620 4 8DG A 601 O2B 162.2 92.5 82.5 REMARK 620 5 8DG A 601 O2A 96.2 93.5 88.9 98.8 REMARK 620 6 HOH A 768 O 85.8 91.6 85.8 78.4 174.3 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 8DG A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 608 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4X5V RELATED DB: PDB REMARK 900 THIS ENTRY IS THE PRE-CATALYTIC COMPLEX. 4X5V IS THE POST-CATALYTIC REMARK 900 COMPLEX DBREF 4XA5 A 251 575 UNP Q9UGP5 DPOLL_HUMAN 251 575 DBREF 4XA5 D 1 4 PDB 4XA5 4XA5 1 4 DBREF 4XA5 P 1 6 PDB 4XA5 4XA5 1 6 DBREF 4XA5 T 1 11 PDB 4XA5 4XA5 1 11 SEQRES 1 A 325 ASN HIS ASN LEU HIS ILE THR GLU LYS LEU GLU VAL LEU SEQRES 2 A 325 ALA LYS ALA TYR SER VAL GLN GLY ASP LYS TRP ARG ALA SEQRES 3 A 325 LEU GLY TYR ALA LYS ALA ILE ASN ALA LEU LYS SER PHE SEQRES 4 A 325 HIS LYS PRO VAL THR SER TYR GLN GLU ALA CAS SER ILE SEQRES 5 A 325 PRO GLY ILE GLY LYS ARG MET ALA GLU LYS ILE ILE GLU SEQRES 6 A 325 ILE LEU GLU SER GLY HIS LEU ARG LYS LEU ASP HIS ILE SEQRES 7 A 325 SER GLU SER VAL PRO VAL LEU GLU LEU PHE SER ASN ILE SEQRES 8 A 325 TRP GLY ALA GLY THR LYS THR ALA GLN MET TRP TYR GLN SEQRES 9 A 325 GLN GLY PHE ARG SER LEU GLU ASP ILE ARG SER GLN ALA SEQRES 10 A 325 SER LEU THR THR GLN GLN ALA ILE GLY LEU LYS HIS TYR SEQRES 11 A 325 SER ASP PHE LEU GLU ARG MET PRO ARG GLU GLU ALA THR SEQRES 12 A 325 GLU ILE GLU GLN THR VAL GLN LYS ALA ALA GLN ALA PHE SEQRES 13 A 325 ASN SER GLY LEU LEU CYS VAL ALA CYS GLY SER TYR ARG SEQRES 14 A 325 ARG GLY LYS ALA THR CYS GLY ASP VAL ASP VAL LEU ILE SEQRES 15 A 325 THR HIS PRO ASP GLY ARG SER HIS ARG GLY ILE PHE SER SEQRES 16 A 325 ARG LEU LEU ASP SER LEU ARG GLN GLU GLY PHE LEU THR SEQRES 17 A 325 ASP ASP LEU VAL SER GLN GLU GLU ASN GLY GLN GLN GLN SEQRES 18 A 325 LYS TYR LEU GLY VAL CYS ARG LEU PRO GLY PRO GLY ARG SEQRES 19 A 325 ARG HIS ARG ARG LEU ASP ILE ILE VAL VAL PRO TYR SER SEQRES 20 A 325 GLU PHE ALA CYS ALA LEU LEU TYR PHE THR GLY SER ALA SEQRES 21 A 325 HIS PHE ASN ARG SER MET ARG ALA LEU ALA LYS THR LYS SEQRES 22 A 325 GLY MET SER LEU SER GLU HIS ALA LEU SER THR ALA VAL SEQRES 23 A 325 VAL ARG ASN THR HIS GLY CYS LYS VAL GLY PRO GLY ARG SEQRES 24 A 325 VAL LEU PRO THR PRO THR GLU LYS ASP VAL PHE ARG LEU SEQRES 25 A 325 LEU GLY LEU PRO TYR ARG GLU PRO ALA GLU ARG ASP TRP SEQRES 1 D 4 DG DC DC DG SEQRES 1 P 6 DC DA DG DT DA DOC SEQRES 1 T 11 DC DG DG DC DA DG DT DA DC DT DG MODRES 4XA5 CAS A 300 CYS MODIFIED RESIDUE HET CAS A 300 9 HET DOC P 6 18 HET 8DG A 601 32 HET MG A 602 1 HET MG A 603 1 HET ACT A 604 4 HET ACT A 605 4 HET ACT A 606 4 HET GOL A 607 6 HET GOL A 608 6 HETNAM CAS S-(DIMETHYLARSENIC)CYSTEINE HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM 8DG 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 CAS C5 H12 AS N O2 S FORMUL 3 DOC C9 H14 N3 O6 P FORMUL 5 8DG C10 H16 N5 O14 P3 FORMUL 6 MG 2(MG 2+) FORMUL 8 ACT 3(C2 H3 O2 1-) FORMUL 11 GOL 2(C3 H8 O3) FORMUL 13 HOH *247(H2 O) HELIX 1 AA1 HIS A 255 GLN A 270 1 16 HELIX 2 AA2 ASP A 272 SER A 288 1 17 HELIX 3 AA3 SER A 295 ILE A 302 1 8 HELIX 4 AA4 GLY A 306 SER A 319 1 14 HELIX 5 AA5 LEU A 322 ILE A 328 5 7 HELIX 6 AA6 SER A 331 ASN A 340 1 10 HELIX 7 AA7 GLY A 345 GLN A 355 1 11 HELIX 8 AA8 SER A 359 ALA A 367 1 9 HELIX 9 AA9 THR A 370 HIS A 379 1 10 HELIX 10 AB1 HIS A 379 GLU A 385 1 7 HELIX 11 AB2 ARG A 389 ASN A 407 1 19 HELIX 12 AB3 CYS A 415 ARG A 420 1 6 HELIX 13 AB4 ILE A 443 GLU A 454 1 12 HELIX 14 AB5 PRO A 495 SER A 497 5 3 HELIX 15 AB6 GLU A 498 GLY A 508 1 11 HELIX 16 AB7 SER A 509 LYS A 523 1 15 HELIX 17 AB8 THR A 555 LEU A 563 1 9 HELIX 18 AB9 GLU A 569 ASP A 574 5 6 SHEET 1 AA1 2 MET A 387 PRO A 388 0 SHEET 2 AA1 2 THR A 424 CYS A 425 -1 O CYS A 425 N MET A 387 SHEET 1 AA2 5 LEU A 411 ALA A 414 0 SHEET 2 AA2 5 VAL A 428 THR A 433 -1 O THR A 433 N LEU A 411 SHEET 3 AA2 5 ARG A 487 VAL A 493 1 O ASP A 490 N VAL A 430 SHEET 4 AA2 5 LYS A 472 CYS A 477 -1 N TYR A 473 O ILE A 491 SHEET 5 AA2 5 LEU A 457 VAL A 462 -1 N LEU A 461 O LEU A 474 SHEET 1 AA3 2 MET A 525 LEU A 527 0 SHEET 2 AA3 2 LEU A 532 THR A 534 -1 O SER A 533 N SER A 526 LINK C ALA A 299 N CAS A 300 1555 1555 1.33 LINK C CAS A 300 N SER A 301 1555 1555 1.34 LINK O SER A 339 MG MG A 603 1555 1555 2.36 LINK O ILE A 341 MG MG A 603 1555 1555 2.39 LINK O ALA A 344 MG MG A 603 1555 1555 2.22 LINK OD1 ASP A 427 MG MG A 602 1555 1555 2.05 LINK OD2 ASP A 429 MG MG A 602 1555 1555 2.31 LINK OP1 DA P 5 MG MG A 603 1555 1555 2.40 LINK O3' DA P 5 P DOC P 6 1555 1555 1.57 LINK O2G 8DG A 601 MG MG A 602 1555 1555 2.15 LINK O2B 8DG A 601 MG MG A 602 1555 1555 2.04 LINK O2A 8DG A 601 MG MG A 602 1555 1555 2.05 LINK MG MG A 602 O HOH A 768 1555 1555 2.10 LINK MG MG A 603 O HOH A 760 1555 1555 2.42 LINK MG MG A 603 O HOH P 110 1555 1555 2.68 CISPEP 1 GLY A 508 SER A 509 0 5.43 SITE 1 AC1 23 ARG A 386 GLY A 416 SER A 417 ARG A 420 SITE 2 AC1 23 GLY A 426 ASP A 427 ASP A 429 TYR A 505 SITE 3 AC1 23 PHE A 506 THR A 507 GLY A 508 ALA A 510 SITE 4 AC1 23 ASN A 513 MG A 602 HOH A 746 HOH A 768 SITE 5 AC1 23 HOH A 785 HOH A 818 HOH A 843 HOH A 877 SITE 6 AC1 23 HOH A 878 DOC P 6 DA T 5 SITE 1 AC2 4 ASP A 427 ASP A 429 8DG A 601 HOH A 768 SITE 1 AC3 6 SER A 339 ILE A 341 ALA A 344 HOH A 760 SITE 2 AC3 6 DA P 5 HOH P 110 SITE 1 AC4 3 ARG A 389 TYR A 418 HOH A 786 SITE 1 AC5 7 HIS A 440 GLY A 442 ILE A 443 PHE A 444 SITE 2 AC5 7 GLY A 468 GLN A 470 VAL A 493 SITE 1 AC6 3 TYR A 267 GLN A 270 SER A 329 SITE 1 AC7 6 ARG A 452 LEU A 457 THR A 458 ASP A 459 SITE 2 AC7 6 ASP A 460 HOH A 874 SITE 1 AC8 7 GLN A 471 VAL A 493 VAL A 494 PRO A 495 SITE 2 AC8 7 HIS A 530 HOH A 770 HOH A 860 CRYST1 55.967 62.340 141.613 90.00 90.00 90.00 P 21 21 21 4 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 0.017868 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016041 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007061 0.00000