PDB Short entry for 5WM8 HEADER TRANSFERASE/DNA 28-JUL-17 5WM8 TITLE STRUCTURE OF THE 10R (+)-CIS-BP-DG MODIFIED REV1 TERNARY COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*(DDG))-3'); COMPND 3 CHAIN: P; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'- COMPND 7 D(P*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3'); COMPND 8 CHAIN: T; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA REPAIR PROTEIN REV1; COMPND 12 CHAIN: A; COMPND 13 SYNONYM: REVERSIONLESS PROTEIN 1; COMPND 14 EC: 2.7.7.-; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 11 S288C); SOURCE 12 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 13 ORGANISM_TAXID: 559292; SOURCE 14 STRAIN: ATCC 204508 / S288C; SOURCE 15 GENE: REV1, YOR346W, O6339; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS KEYWDS BENZO[A]PYRENE REV1 POLYMERASE CARCINOGEN LESION BYPASS, DNA BINDING KEYWDS 2 PROTEIN, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR O.RECHKOBLIT,A.KOLBANOVSKY,H.LANDES,N.E.GEACINTOV,A.K.AGGARWAL REVDAT 4 04-OCT-23 5WM8 1 LINK REVDAT 3 18-DEC-19 5WM8 1 REMARK REVDAT 2 01-NOV-17 5WM8 1 JRNL REVDAT 1 25-OCT-17 5WM8 0 JRNL AUTH O.RECHKOBLIT,A.KOLBANOVSKIY,H.LANDES,N.E.GEACINTOV, JRNL AUTH 2 A.K.AGGARWAL JRNL TITL MECHANISM OF ERROR-FREE REPLICATION ACROSS BENZO[A]PYRENE JRNL TITL 2 STEREOISOMERS BY REV1 DNA POLYMERASE. JRNL REF NAT COMMUN V. 8 965 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 29042535 JRNL DOI 10.1038/S41467-017-01013-5 REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 43093 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) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2290 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) : 1.93 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2944 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.48 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 161 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3434 REMARK 3 NUCLEIC ACID ATOMS : 571 REMARK 3 HETEROGEN ATOMS : 123 REMARK 3 SOLVENT ATOMS : 311 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.45000 REMARK 3 B22 (A**2) : -0.25000 REMARK 3 B33 (A**2) : 0.69000 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): 0.149 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.138 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.091 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.126 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4351 ; 0.010 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 3763 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5977 ; 1.394 ; 1.869 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8774 ; 0.988 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 449 ; 5.772 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 159 ;36.342 ;24.025 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 652 ;13.654 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;17.164 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 639 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4333 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 895 ; 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): 1757 ; 1.728 ; 2.973 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1756 ; 1.727 ; 2.972 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2204 ; 2.710 ; 4.445 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2205 ; 2.710 ; 4.447 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2592 ; 2.196 ; 3.430 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2592 ; 2.195 ; 3.430 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3769 ; 3.512 ; 5.068 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5107 ; 5.409 ;35.276 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5037 ; 5.252 ;34.935 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 : NULL 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 5WM8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1000229274. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.100 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45446 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 2AQ4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.25 M SODIUM CITRATE PH 6.0 BUFFER 15 REMARK 280 -20% PEG3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 31.27550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 90.17900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.27550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 90.17900 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: P, T, A 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 LYS A 305 REMARK 465 ARG A 306 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 DC T 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DC T 1 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC T 1 C6 REMARK 470 THR A 348 OG1 CG2 REMARK 470 LYS A 353 CG CD CE NZ REMARK 470 ILE A 479 CG1 CG2 CD1 REMARK 470 LYS A 673 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 OE1 GLN A 495 O HOH A 901 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 DC T 1 O3' DA T 2 P -0.119 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 ASP A 362 CB - CG - OD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 CYS A 382 CA - CB - SG ANGL. DEV. = 7.5 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 THR A 348 62.34 -111.50 REMARK 500 CYS A 365 64.15 24.64 REMARK 500 LYS A 396 -93.02 -129.21 REMARK 500 ASN A 397 46.03 -94.07 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 P 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA P 11 OP1 REMARK 620 2 DA P 11 OP1 4.3 REMARK 620 3 HOH P 209 O 93.4 96.1 REMARK 620 4 ASP A 548 O 169.2 172.7 84.5 REMARK 620 5 LEU A 550 O 84.0 81.6 175.4 97.2 REMARK 620 6 VAL A 553 O 95.8 92.2 95.5 95.0 88.6 REMARK 620 7 HOH A1125 O 84.0 87.5 86.5 85.2 89.4 178.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 802 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 362 OD2 REMARK 620 2 PHE A 363 O 88.8 REMARK 620 3 ASP A 467 OD2 100.8 93.0 REMARK 620 4 DCP A 804 O3G 81.1 95.1 171.7 REMARK 620 5 DCP A 804 O2A 87.7 165.5 101.4 70.5 REMARK 620 6 DCP A 804 O2B 165.4 96.4 92.5 84.9 83.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 803 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 362 OD2 REMARK 620 2 DCP A 804 O3G 81.5 REMARK 620 3 DCP A 804 O2A 76.7 82.3 REMARK 620 4 HOH A1019 O 97.8 174.1 103.2 REMARK 620 5 HOH A1091 O 80.9 113.0 150.6 61.2 REMARK 620 6 HOH A1097 O 171.0 91.4 108.0 88.7 96.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 801 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 467 OD1 REMARK 620 2 ASP A 467 OD2 48.5 REMARK 620 3 GLU A 468 OE2 130.3 134.8 REMARK 620 4 DCP A 804 O2A 113.8 68.4 106.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG P 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BAP T 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DCP A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 806 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 807 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 808 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 809 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 810 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 811 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 812 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 813 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 814 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 815 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 816 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 817 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 818 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5WM1 RELATED DB: PDB REMARK 900 5WM1 CONTAINS THE SAME REV1 PROTEIN/DNA-DCTP TERNARY COMPLEX BUT REMARK 900 THE TEMPLATE GUANINE IS MODIFIED BY THE 10S (+)-TRANS-BP REMARK 900 STEREOISOMER DBREF 5WM8 P 1 12 PDB 5WM8 5WM8 1 12 DBREF 5WM8 T 1 17 PDB 5WM8 5WM8 1 17 DBREF 5WM8 A 305 738 UNP P12689 REV1_YEAST 305 738 SEQRES 1 P 12 DG DG DG DG DT DG DT DG DG DT DA DDG SEQRES 1 T 17 DC DA DT DC DG DC DT DA DC DC DA DC DA SEQRES 2 T 17 DC DC DC DC SEQRES 1 A 434 LYS ARG ILE VAL ALA CYS ASP ASP PRO ASP PHE LEU THR SEQRES 2 A 434 SER TYR PHE ALA HIS SER ARG LEU HIS HIS LEU SER ALA SEQRES 3 A 434 TRP LYS ALA ASN LEU LYS ASP LYS PHE LEU ASN GLU ASN SEQRES 4 A 434 ILE HIS LYS TYR THR LYS ILE THR ASP LYS ASP THR TYR SEQRES 5 A 434 ILE ILE PHE HIS ILE ASP PHE ASP CYS PHE PHE ALA THR SEQRES 6 A 434 VAL ALA TYR LEU CYS ARG SER SER SER PHE SER ALA CYS SEQRES 7 A 434 ASP PHE LYS ARG ASP PRO ILE VAL VAL CYS HIS GLY THR SEQRES 8 A 434 LYS ASN SER ASP ILE ALA SER CYS ASN TYR VAL ALA ARG SEQRES 9 A 434 SER TYR GLY ILE LYS ASN GLY MET TRP VAL SER GLN ALA SEQRES 10 A 434 GLU LYS MET LEU PRO ASN GLY ILE LYS LEU ILE SER LEU SEQRES 11 A 434 PRO TYR THR PHE GLU GLN PHE GLN LEU LYS SER GLU ALA SEQRES 12 A 434 PHE TYR SER THR LEU LYS ARG LEU ASN ILE PHE ASN LEU SEQRES 13 A 434 ILE LEU PRO ILE SER ILE ASP GLU ALA VAL CYS VAL ARG SEQRES 14 A 434 ILE ILE PRO ASP ASN ILE HIS ASN THR ASN THR LEU ASN SEQRES 15 A 434 ALA ARG LEU CYS GLU GLU ILE ARG GLN GLU ILE PHE GLN SEQRES 16 A 434 GLY THR ASN GLY CYS THR VAL SER ILE GLY CYS SER ASP SEQRES 17 A 434 SER LEU VAL LEU ALA ARG LEU ALA LEU LYS MET ALA LYS SEQRES 18 A 434 PRO ASN GLY TYR ASN ILE THR PHE LYS SER ASN LEU SER SEQRES 19 A 434 GLU GLU PHE TRP SER SER PHE LYS LEU ASP ASP LEU PRO SEQRES 20 A 434 GLY VAL GLY HIS SER THR LEU SER ARG LEU GLU SER THR SEQRES 21 A 434 PHE ASP SER PRO HIS SER LEU ASN ASP LEU ARG LYS ARG SEQRES 22 A 434 TYR THR LEU ASP ALA LEU LYS ALA SER VAL GLY SER LYS SEQRES 23 A 434 LEU GLY MET LYS ILE HIS LEU ALA LEU GLN GLY GLN ASP SEQRES 24 A 434 ASP GLU GLU SER LEU LYS ILE LEU TYR ASP PRO LYS GLU SEQRES 25 A 434 VAL LEU GLN ARG LYS SER LEU SER ILE ASP ILE ASN TRP SEQRES 26 A 434 GLY ILE ARG PHE LYS ASN ILE THR GLN VAL ASP LEU PHE SEQRES 27 A 434 ILE GLU ARG GLY CYS GLN TYR LEU LEU GLU LYS LEU ASN SEQRES 28 A 434 GLU ILE ASN LYS THR THR SER GLN ILE THR LEU LYS LEU SEQRES 29 A 434 MET ARG ARG CYS LYS ASP ALA PRO ILE GLU PRO PRO LYS SEQRES 30 A 434 TYR MET GLY MET GLY ARG CYS ASP SER PHE SER ARG SER SEQRES 31 A 434 SER ARG LEU GLY ILE PRO THR ASN GLU PHE GLY ILE ILE SEQRES 32 A 434 ALA THR GLU MET LYS SER LEU TYR ARG THR LEU GLY CYS SEQRES 33 A 434 PRO PRO MET GLU LEU ARG GLY LEU ALA LEU GLN PHE ASN SEQRES 34 A 434 LYS LEU VAL ASP VAL HET DDG P 12 31 HET MG P 101 1 HET BAP T 101 23 HET MG A 801 1 HET MG A 802 1 HET MG A 803 1 HET DCP A 804 28 HET GOL A 805 6 HET GOL A 806 6 HET GOL A 807 6 HET EDO A 808 4 HET EDO A 809 4 HET EDO A 810 4 HET EDO A 811 4 HET EDO A 812 8 HET EDO A 813 4 HET EDO A 814 4 HET EDO A 815 4 HET EDO A 816 4 HET PEG A 817 7 HET PEG A 818 7 HETNAM DDG 2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM BAP 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE HETNAM DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 DDG C10 H14 N5 O6 P FORMUL 4 MG 4(MG 2+) FORMUL 5 BAP C20 H16 O3 FORMUL 9 DCP C9 H16 N3 O13 P3 FORMUL 10 GOL 3(C3 H8 O3) FORMUL 13 EDO 9(C2 H6 O2) FORMUL 22 PEG 2(C4 H10 O3) FORMUL 24 HOH *311(H2 O) HELIX 1 AA1 ASP A 314 SER A 323 1 10 HELIX 2 AA2 SER A 323 ASN A 343 1 21 HELIX 3 AA3 CYS A 365 CYS A 374 1 10 HELIX 4 AA4 SER A 376 SER A 380 5 5 HELIX 5 AA5 ASN A 404 TYR A 410 1 7 HELIX 6 AA6 TRP A 417 MET A 424 1 8 HELIX 7 AA7 THR A 437 LEU A 455 1 19 HELIX 8 AA8 THR A 482 THR A 501 1 20 HELIX 9 AA9 SER A 513 LYS A 525 1 13 HELIX 10 AB1 PHE A 533 LEU A 537 5 5 HELIX 11 AB2 SER A 538 SER A 543 1 6 HELIX 12 AB3 SER A 544 PHE A 545 5 2 HELIX 13 AB4 LYS A 546 LEU A 550 5 5 HELIX 14 AB5 GLY A 554 PHE A 565 1 12 HELIX 15 AB6 SER A 570 TYR A 578 1 9 HELIX 16 AB7 THR A 579 GLY A 588 1 10 HELIX 17 AB8 GLY A 588 LEU A 599 1 12 HELIX 18 AB9 ASP A 604 ASP A 613 1 10 HELIX 19 AC1 ASP A 613 LEU A 618 1 6 HELIX 20 AC2 ASN A 635 ILE A 657 1 23 HELIX 21 AC3 GLU A 703 LEU A 718 1 16 HELIX 22 AC4 PRO A 721 MET A 723 5 3 SHEET 1 AA1 5 LEU A 460 SER A 465 0 SHEET 2 AA1 5 GLU A 468 ILE A 475 -1 O VAL A 470 N LEU A 462 SHEET 3 AA1 5 THR A 355 PHE A 363 -1 N PHE A 359 O CYS A 471 SHEET 4 AA1 5 VAL A 506 SER A 511 -1 O SER A 511 N ILE A 358 SHEET 5 AA1 5 TYR A 529 ILE A 531 1 O ASN A 530 N CYS A 510 SHEET 1 AA2 3 SER A 402 CYS A 403 0 SHEET 2 AA2 3 ILE A 389 VAL A 391 -1 N VAL A 391 O SER A 402 SHEET 3 AA2 3 ILE A 432 LEU A 434 1 O LEU A 434 N VAL A 390 SHEET 1 AA3 4 LEU A 623 ILE A 627 0 SHEET 2 AA3 4 LEU A 725 ASP A 737 -1 O PHE A 732 N LEU A 623 SHEET 3 AA3 4 LYS A 659 ARG A 671 -1 N MET A 669 O ARG A 726 SHEET 4 AA3 4 CYS A 688 THR A 701 -1 O PHE A 691 N LEU A 668 LINK O3'A DA P 11 P ADDG P 12 1555 1555 1.57 LINK O3'B DA P 11 P BDDG P 12 1555 1555 1.60 LINK N2 DG T 5 C4' BAP T 101 1555 1555 1.34 LINK OP1A DA P 11 MG MG P 101 1555 1555 2.68 LINK OP1B DA P 11 MG MG P 101 1555 1555 2.54 LINK MG MG P 101 O HOH P 209 1555 1555 2.28 LINK MG MG P 101 O ASP A 548 1555 1555 2.21 LINK MG MG P 101 O LEU A 550 1555 1555 2.68 LINK MG MG P 101 O VAL A 553 1555 1555 2.21 LINK MG MG P 101 O HOH A1125 1555 1555 2.77 LINK OD2 ASP A 362 MG MG A 802 1555 1555 2.00 LINK OD2 ASP A 362 MG MG A 803 1555 1555 2.47 LINK O PHE A 363 MG MG A 802 1555 1555 2.24 LINK OD1 ASP A 467 MG MG A 801 1555 1555 1.97 LINK OD2 ASP A 467 MG MG A 801 1555 1555 2.99 LINK OD2 ASP A 467 MG MG A 802 1555 1555 2.24 LINK OE2 GLU A 468 MG MG A 801 1555 1555 2.76 LINK MG MG A 801 O2A DCP A 804 1555 1555 2.90 LINK MG MG A 802 O3G DCP A 804 1555 1555 2.48 LINK MG MG A 802 O2A DCP A 804 1555 1555 2.03 LINK MG MG A 802 O2B DCP A 804 1555 1555 2.03 LINK MG MG A 803 O3G DCP A 804 1555 1555 2.00 LINK MG MG A 803 O2A DCP A 804 1555 1555 2.00 LINK MG MG A 803 O HOH A1019 1555 1555 2.62 LINK MG MG A 803 O HOH A1091 1555 1555 2.55 LINK MG MG A 803 O HOH A1097 1555 1555 2.33 CISPEP 1 LYS A 525 PRO A 526 0 -2.86 SITE 1 AC1 6 ASP A 548 LEU A 550 VAL A 553 HOH A1125 SITE 2 AC1 6 DA P 11 HOH P 209 SITE 1 AC2 8 ASP A 399 TRP A 417 LYS A 681 EDO A 811 SITE 2 AC2 8 PEG A 817 HOH A 978 HOH A1008 DG T 5 SITE 1 AC3 6 ASP A 362 ASP A 467 GLU A 468 MG A 802 SITE 2 AC3 6 DCP A 804 DDG P 12 SITE 1 AC4 6 ASP A 362 PHE A 363 ASP A 467 MG A 801 SITE 2 AC4 6 MG A 803 DCP A 804 SITE 1 AC5 6 ASP A 362 MG A 802 DCP A 804 HOH A1019 SITE 2 AC5 6 HOH A1091 HOH A1097 SITE 1 AC6 26 ARG A 324 LEU A 328 ASP A 362 PHE A 363 SITE 2 AC6 26 ASP A 364 CYS A 365 PHE A 366 PHE A 367 SITE 3 AC6 26 ALA A 401 SER A 402 TYR A 405 ARG A 408 SITE 4 AC6 26 ASN A 414 ASP A 467 LYS A 525 MG A 801 SITE 5 AC6 26 MG A 802 MG A 803 GOL A 807 HOH A 942 SITE 6 AC6 26 HOH A 948 HOH A1001 HOH A1049 HOH A1050 SITE 7 AC6 26 HOH A1097 DDG P 12 SITE 1 AC7 5 TRP A 331 ASN A 334 LEU A 335 GLN A 442 SITE 2 AC7 5 SER A 445 SITE 1 AC8 5 LEU A 335 LYS A 338 TYR A 449 ILE A 461 SITE 2 AC8 5 HOH A1022 SITE 1 AC9 6 ARG A 324 GLY A 415 DCP A 804 HOH A 902 SITE 2 AC9 6 HOH A 913 DDG P 12 SITE 1 AD1 4 VAL A 308 SER A 318 TYR A 319 DC T 4 SITE 1 AD2 5 ARG A 488 PHE A 691 SER A 692 LEU A 718 SITE 2 AD2 5 HOH A1145 SITE 1 AD3 2 ASN A 527 HOH A 984 SITE 1 AD4 4 MET A 416 TRP A 417 GLN A 420 BAP T 101 SITE 1 AD5 8 CYS A 365 PHE A 384 LYS A 385 PRO A 526 SITE 2 AD5 8 HOH A 932 HOH A 988 HOH A1034 HOH A1065 SITE 1 AD6 7 HIS A 326 SER A 624 TYR A 649 HOH A 930 SITE 2 AD6 7 HOH A1144 DT T 7 DA T 8 SITE 1 AD7 7 SER A 378 PHE A 379 SER A 380 ALA A 381 SITE 2 AD7 7 CYS A 382 GLU A 678 PRO A 679 SITE 1 AD8 7 SER A 622 GLN A 731 ASN A 733 HOH A 991 SITE 2 AD8 7 DC T 9 HOH T 201 HOH T 211 SITE 1 AD9 1 ASP A 352 SITE 1 AE1 5 HOH A 978 HOH A 998 HOH A1102 HOH A1121 SITE 2 AE1 5 BAP T 101 SITE 1 AE2 2 GLN A 499 ASN A 502 CRYST1 62.551 180.358 54.586 90.00 90.00 90.00 P 21 21 2 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 0.015987 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005545 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018320 0.00000