HEADER TRANSFERASE/DNA 21-JAN-20 6VKP TITLE CRYSTAL STRUCTURE OF DPO4 EXTENSION PAST 8-OXOADENINE (OXOA) AND DG COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*AP*GP*AP*TP*TP*CP*G)-3'); COMPND 3 CHAIN: P, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*TP*TP*CP*AP*TP*(A38) COMPND 7 P*GP*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*CP*C)-3'); COMPND 8 CHAIN: T, C; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA POLYMERASE IV; COMPND 12 CHAIN: A, D; COMPND 13 SYNONYM: POL IV; COMPND 14 EC: 2.7.7.7; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: SACCHAROLOBUS SOLFATARICUS; SOURCE 13 ORGANISM_TAXID: 2287; SOURCE 14 GENE: DBH, SSOP1_2570, SULA_0242, SULB_0243, SULC_0242, SULG_01230, SOURCE 15 SULH_01230, SULI_01230, SULM_01230, SULN_01230, SULO_01240, SOURCE 16 SULZ_01250; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DPO4, Y-FAMILY DNA POLYMERASE, TRANSLESION SYNTHESIS, TRANSFERASE, KEYWDS 2 EXTENSION, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.JUNG,S.LEE REVDAT 3 11-OCT-23 6VKP 1 REMARK REVDAT 2 11-AUG-21 6VKP 1 JRNL REVDAT 1 27-JAN-21 6VKP 0 JRNL AUTH H.JUNG,S.LEE JRNL TITL INSIGHTS INTO THE MISMATCH DISCRIMINATION MECHANISM OF JRNL TITL 2 Y-FAMILY DNA POLYMERASE DPO4. JRNL REF BIOCHEM.J. V. 478 1769 2021 JRNL REFN ESSN 1470-8728 JRNL PMID 33881499 JRNL DOI 10.1042/BCJ20210162 REMARK 2 REMARK 2 RESOLUTION. 2.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 35516 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.220 REMARK 3 FREE R VALUE TEST SET COUNT : 1855 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 2.6000 - 2.5400 0.95 2432 157 0.3250 0.3526 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.78 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 : 0.010 7088 REMARK 3 ANGLE : 1.239 9808 REMARK 3 CHIRALITY : 0.096 1120 REMARK 3 PLANARITY : 0.006 1012 REMARK 3 DIHEDRAL : 25.364 2922 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6VKP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1000246580. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35565 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.530 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.57 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 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1JX4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM TRIS 7.5 18% PEG 3350 100 MM REMARK 280 MAGNESIUM ACETATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 51.84500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 5490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 5570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, D 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 DT T 1 REMARK 465 DT C 1 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 B 12 O3' DC B 12 C3' -0.040 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 DG P 0 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG P 2 O3' - P - OP2 ANGL. DEV. = -18.8 DEGREES REMARK 500 DG P 2 O3' - P - OP1 ANGL. DEV. = -23.3 DEGREES REMARK 500 DG P 2 OP1 - P - OP2 ANGL. DEV. = 9.7 DEGREES REMARK 500 DC P 12 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT T 5 C3' - O3' - P ANGL. DEV. = 12.5 DEGREES REMARK 500 A38 T 6 C3' - O3' - P ANGL. DEV. = 38.8 DEGREES REMARK 500 DG T 7 O3' - P - OP2 ANGL. DEV. = 22.0 DEGREES REMARK 500 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG B 4 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT C 2 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 A38 C 6 O3' - P - O5' ANGL. DEV. = 17.9 DEGREES REMARK 500 A38 C 6 C3' - O3' - P ANGL. DEV. = 26.9 DEGREES REMARK 500 DC C 19 O4' - C1' - N1 ANGL. DEV. = 1.9 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 TYR A 10 58.02 28.28 REMARK 500 SER A 22 3.29 -68.14 REMARK 500 LEU A 68 74.73 -115.61 REMARK 500 ARG A 77 78.60 -104.68 REMARK 500 ARG A 93 0.59 -60.05 REMARK 500 SER A 96 153.69 176.52 REMARK 500 ASP A 105 14.68 -140.90 REMARK 500 SER A 145 -169.37 -167.38 REMARK 500 ASN A 161 62.53 36.19 REMARK 500 ASP A 277 78.80 52.79 REMARK 500 LYS A 278 -19.84 80.48 REMARK 500 GLU A 324 -74.46 -59.40 REMARK 500 TYR D 10 59.14 25.74 REMARK 500 ARG D 36 -80.44 -56.30 REMARK 500 ARG D 77 76.95 -109.88 REMARK 500 SER D 96 143.97 -178.22 REMARK 500 ASP D 105 11.95 -142.47 REMARK 500 ASP D 117 -157.08 -135.13 REMARK 500 ASP D 277 82.47 51.09 REMARK 500 LYS D 278 -24.98 75.69 REMARK 500 LYS D 339 72.24 57.80 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 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH P 103 O REMARK 620 2 ASP A 7 OD2 162.0 REMARK 620 3 ASP A 105 OD1 104.8 92.4 REMARK 620 4 GLU A 106 OE2 98.7 71.6 135.2 REMARK 620 5 DZ4 A 403 O1A 92.7 83.8 83.8 132.8 REMARK 620 6 HOH A 507 O 87.6 74.4 156.1 60.0 75.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD1 REMARK 620 2 PHE A 8 O 83.8 REMARK 620 3 ASP A 105 OD2 95.1 80.9 REMARK 620 4 DZ4 A 403 O1A 104.3 158.7 78.9 REMARK 620 5 DZ4 A 403 O2G 92.6 114.0 164.0 85.7 REMARK 620 6 DZ4 A 403 O2B 171.9 89.3 87.9 83.6 86.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 105 O REMARK 620 2 ASP D 7 OD2 167.3 REMARK 620 3 ASP D 105 OD1 93.0 91.9 REMARK 620 4 GLU D 106 OE2 92.8 74.6 122.1 REMARK 620 5 DZ4 D 403 O1A 99.1 92.1 95.0 140.3 REMARK 620 6 HOH D 505 O 102.4 72.9 164.6 57.5 83.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP D 7 OD1 REMARK 620 2 PHE D 8 O 83.7 REMARK 620 3 ASP D 105 OD2 104.1 99.6 REMARK 620 4 DZ4 D 403 O2B 171.7 98.9 83.2 REMARK 620 5 DZ4 D 403 O1A 99.3 168.2 68.5 79.7 REMARK 620 6 DZ4 D 403 O1G 86.4 112.7 147.0 85.4 79.0 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 MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DZ4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG D 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG D 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DZ4 D 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DT C 5 and A38 C REMARK 800 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide A38 C 6 and DG C REMARK 800 7 DBREF 6VKP P 0 13 PDB 6VKP 6VKP 0 13 DBREF 6VKP T 1 19 PDB 6VKP 6VKP 1 19 DBREF1 6VKP A 1 341 UNP A0A0E3K6E9_SACSO DBREF2 6VKP A A0A0E3K6E9 1 341 DBREF 6VKP B 0 13 PDB 6VKP 6VKP 0 13 DBREF 6VKP C 1 19 PDB 6VKP 6VKP 1 19 DBREF1 6VKP D 1 341 UNP A0A0E3K6E9_SACSO DBREF2 6VKP D A0A0E3K6E9 1 341 SEQRES 1 P 14 DG DG DG DG DG DA DA DA DG DA DT DT DC SEQRES 2 P 14 DG SEQRES 1 T 19 DT DT DC DA DT A38 DG DA DA DT DC DT DT SEQRES 2 T 19 DT DC DC DC DC DC SEQRES 1 A 341 MET ILE VAL LEU PHE VAL ASP PHE ASP TYR PHE TYR ALA SEQRES 2 A 341 GLN VAL GLU GLU VAL LEU ASN PRO SER LEU LYS GLY LYS SEQRES 3 A 341 PRO VAL VAL VAL CYS VAL PHE SER GLY ARG PHE GLU ASP SEQRES 4 A 341 SER GLY ALA VAL ALA THR ALA ASN TYR GLU ALA ARG LYS SEQRES 5 A 341 PHE GLY VAL LYS ALA GLY ILE PRO ILE VAL GLU ALA LYS SEQRES 6 A 341 LYS ILE LEU PRO ASN ALA VAL TYR LEU PRO MET ARG LYS SEQRES 7 A 341 GLU VAL TYR GLN GLN VAL SER SER ARG ILE MET ASN LEU SEQRES 8 A 341 LEU ARG GLU TYR SER GLU LYS ILE GLU ILE ALA SER ILE SEQRES 9 A 341 ASP GLU ALA TYR LEU ASP ILE SER ASP LYS VAL ARG ASP SEQRES 10 A 341 TYR ARG GLU ALA TYR ASN LEU GLY LEU GLU ILE LYS ASN SEQRES 11 A 341 LYS ILE LEU GLU LYS GLU LYS ILE THR VAL THR VAL GLY SEQRES 12 A 341 ILE SER LYS ASN LYS VAL PHE ALA LYS ILE ALA ALA ASP SEQRES 13 A 341 MET ALA LYS PRO ASN GLY ILE LYS VAL ILE ASP ASP GLU SEQRES 14 A 341 GLU VAL LYS ARG LEU ILE ARG GLU LEU ASP ILE ALA ASP SEQRES 15 A 341 VAL PRO GLY ILE GLY ASN ILE THR ALA GLU LYS LEU LYS SEQRES 16 A 341 LYS LEU GLY ILE ASN LYS LEU VAL ASP THR LEU SER ILE SEQRES 17 A 341 GLU PHE ASP LYS LEU LYS GLY MET ILE GLY GLU ALA LYS SEQRES 18 A 341 ALA LYS TYR LEU ILE SER LEU ALA ARG ASP GLU TYR ASN SEQRES 19 A 341 GLU PRO ILE ARG THR ARG VAL ARG LYS SER ILE GLY ARG SEQRES 20 A 341 ILE VAL THR MET LYS ARG ASN SER ARG ASN LEU GLU GLU SEQRES 21 A 341 ILE LYS PRO TYR LEU PHE ARG ALA ILE GLU GLU SER TYR SEQRES 22 A 341 TYR LYS LEU ASP LYS ARG ILE PRO LYS ALA ILE HIS VAL SEQRES 23 A 341 VAL ALA VAL THR GLU ASP LEU ASP ILE VAL SER ARG GLY SEQRES 24 A 341 ARG THR PHE PRO HIS GLY ILE SER LYS GLU THR ALA TYR SEQRES 25 A 341 SER GLU SER VAL LYS LEU LEU GLN LYS ILE LEU GLU GLU SEQRES 26 A 341 ASP GLU ARG LYS ILE ARG ARG ILE GLY VAL ARG PHE SER SEQRES 27 A 341 LYS PHE ILE SEQRES 1 B 14 DG DG DG DG DG DA DA DA DG DA DT DT DC SEQRES 2 B 14 DG SEQRES 1 C 19 DT DT DC DA DT A38 DG DA DA DT DC DT DT SEQRES 2 C 19 DT DC DC DC DC DC SEQRES 1 D 341 MET ILE VAL LEU PHE VAL ASP PHE ASP TYR PHE TYR ALA SEQRES 2 D 341 GLN VAL GLU GLU VAL LEU ASN PRO SER LEU LYS GLY LYS SEQRES 3 D 341 PRO VAL VAL VAL CYS VAL PHE SER GLY ARG PHE GLU ASP SEQRES 4 D 341 SER GLY ALA VAL ALA THR ALA ASN TYR GLU ALA ARG LYS SEQRES 5 D 341 PHE GLY VAL LYS ALA GLY ILE PRO ILE VAL GLU ALA LYS SEQRES 6 D 341 LYS ILE LEU PRO ASN ALA VAL TYR LEU PRO MET ARG LYS SEQRES 7 D 341 GLU VAL TYR GLN GLN VAL SER SER ARG ILE MET ASN LEU SEQRES 8 D 341 LEU ARG GLU TYR SER GLU LYS ILE GLU ILE ALA SER ILE SEQRES 9 D 341 ASP GLU ALA TYR LEU ASP ILE SER ASP LYS VAL ARG ASP SEQRES 10 D 341 TYR ARG GLU ALA TYR ASN LEU GLY LEU GLU ILE LYS ASN SEQRES 11 D 341 LYS ILE LEU GLU LYS GLU LYS ILE THR VAL THR VAL GLY SEQRES 12 D 341 ILE SER LYS ASN LYS VAL PHE ALA LYS ILE ALA ALA ASP SEQRES 13 D 341 MET ALA LYS PRO ASN GLY ILE LYS VAL ILE ASP ASP GLU SEQRES 14 D 341 GLU VAL LYS ARG LEU ILE ARG GLU LEU ASP ILE ALA ASP SEQRES 15 D 341 VAL PRO GLY ILE GLY ASN ILE THR ALA GLU LYS LEU LYS SEQRES 16 D 341 LYS LEU GLY ILE ASN LYS LEU VAL ASP THR LEU SER ILE SEQRES 17 D 341 GLU PHE ASP LYS LEU LYS GLY MET ILE GLY GLU ALA LYS SEQRES 18 D 341 ALA LYS TYR LEU ILE SER LEU ALA ARG ASP GLU TYR ASN SEQRES 19 D 341 GLU PRO ILE ARG THR ARG VAL ARG LYS SER ILE GLY ARG SEQRES 20 D 341 ILE VAL THR MET LYS ARG ASN SER ARG ASN LEU GLU GLU SEQRES 21 D 341 ILE LYS PRO TYR LEU PHE ARG ALA ILE GLU GLU SER TYR SEQRES 22 D 341 TYR LYS LEU ASP LYS ARG ILE PRO LYS ALA ILE HIS VAL SEQRES 23 D 341 VAL ALA VAL THR GLU ASP LEU ASP ILE VAL SER ARG GLY SEQRES 24 D 341 ARG THR PHE PRO HIS GLY ILE SER LYS GLU THR ALA TYR SEQRES 25 D 341 SER GLU SER VAL LYS LEU LEU GLN LYS ILE LEU GLU GLU SEQRES 26 D 341 ASP GLU ARG LYS ILE ARG ARG ILE GLY VAL ARG PHE SER SEQRES 27 D 341 LYS PHE ILE HET A38 T 6 22 HET A38 C 6 22 HET MG A 401 1 HET MG A 402 1 HET DZ4 A 403 30 HET MG D 401 1 HET MG D 402 1 HET DZ4 D 403 30 HETNAM A38 8-OXY DEOXYADENOSINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM DZ4 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 DZ4 PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE FORMUL 2 A38 2(C10 H14 N5 O7 P) FORMUL 7 MG 4(MG 2+) FORMUL 9 DZ4 2(C10 H17 N6 O11 P3) FORMUL 13 HOH *65(H2 O) HELIX 1 AA1 TYR A 10 ASN A 20 1 11 HELIX 2 AA2 PRO A 21 LYS A 24 5 4 HELIX 3 AA3 ASN A 47 LYS A 52 1 6 HELIX 4 AA4 PRO A 60 LEU A 68 1 9 HELIX 5 AA5 ARG A 77 ARG A 93 1 17 HELIX 6 AA6 ASP A 117 LYS A 137 1 21 HELIX 7 AA7 ASN A 147 ALA A 158 1 12 HELIX 8 AA8 ASP A 167 LEU A 178 1 12 HELIX 9 AA9 ASP A 179 VAL A 183 5 5 HELIX 10 AB1 GLY A 187 LYS A 196 1 10 HELIX 11 AB2 LYS A 201 SER A 207 5 7 HELIX 12 AB3 GLU A 209 GLY A 218 1 10 HELIX 13 AB4 GLY A 218 ARG A 230 1 13 HELIX 14 AB5 ASN A 257 ASP A 277 1 21 HELIX 15 AB6 SER A 307 ASP A 326 1 20 HELIX 16 AB7 TYR D 10 ASN D 20 1 11 HELIX 17 AB8 PRO D 21 LYS D 24 5 4 HELIX 18 AB9 ASN D 47 LYS D 52 1 6 HELIX 19 AC1 PRO D 60 LEU D 68 1 9 HELIX 20 AC2 ARG D 77 LEU D 92 1 16 HELIX 21 AC3 ASP D 117 GLU D 136 1 20 HELIX 22 AC4 ASN D 147 ALA D 158 1 12 HELIX 23 AC5 ASP D 167 LEU D 178 1 12 HELIX 24 AC6 ASP D 179 VAL D 183 5 5 HELIX 25 AC7 GLY D 187 LYS D 196 1 10 HELIX 26 AC8 LYS D 201 SER D 207 5 7 HELIX 27 AC9 GLU D 209 GLY D 218 1 10 HELIX 28 AD1 GLY D 218 ARG D 230 1 13 HELIX 29 AD2 ASN D 257 ASP D 277 1 21 HELIX 30 AD3 SER D 307 ASP D 326 1 20 SHEET 1 AA1 5 ILE A 99 ILE A 101 0 SHEET 2 AA1 5 GLU A 106 ASP A 110 -1 O TYR A 108 N GLU A 100 SHEET 3 AA1 5 VAL A 3 PHE A 8 -1 N LEU A 4 O LEU A 109 SHEET 4 AA1 5 VAL A 140 SER A 145 -1 O GLY A 143 N PHE A 5 SHEET 5 AA1 5 ILE A 163 VAL A 165 1 O LYS A 164 N VAL A 142 SHEET 1 AA2 3 GLY A 41 ALA A 46 0 SHEET 2 AA2 3 VAL A 28 PHE A 33 -1 N VAL A 32 O ALA A 42 SHEET 3 AA2 3 VAL A 72 PRO A 75 1 O LEU A 74 N CYS A 31 SHEET 1 AA3 4 SER A 244 SER A 255 0 SHEET 2 AA3 4 ILE A 330 PHE A 340 -1 O ILE A 333 N VAL A 249 SHEET 3 AA3 4 PRO A 281 THR A 290 -1 N VAL A 289 O ARG A 331 SHEET 4 AA3 4 ILE A 295 THR A 301 -1 O VAL A 296 N ALA A 288 SHEET 1 AA4 5 ILE D 99 ILE D 101 0 SHEET 2 AA4 5 GLU D 106 ASP D 110 -1 O TYR D 108 N GLU D 100 SHEET 3 AA4 5 VAL D 3 PHE D 8 -1 N LEU D 4 O LEU D 109 SHEET 4 AA4 5 VAL D 140 SER D 145 -1 O GLY D 143 N PHE D 5 SHEET 5 AA4 5 ILE D 163 VAL D 165 1 O LYS D 164 N ILE D 144 SHEET 1 AA5 3 GLY D 41 ALA D 46 0 SHEET 2 AA5 3 VAL D 28 PHE D 33 -1 N VAL D 32 O ALA D 42 SHEET 3 AA5 3 VAL D 72 PRO D 75 1 O LEU D 74 N CYS D 31 SHEET 1 AA6 4 SER D 244 SER D 255 0 SHEET 2 AA6 4 ILE D 330 PHE D 340 -1 O PHE D 337 N ILE D 245 SHEET 3 AA6 4 PRO D 281 THR D 290 -1 N VAL D 289 O ARG D 331 SHEET 4 AA6 4 ILE D 295 THR D 301 -1 O VAL D 296 N ALA D 288 LINK O3' DT T 5 P A38 T 6 1555 1555 1.56 LINK O3' A38 T 6 P DG T 7 1555 1555 1.66 LINK O3' DT C 5 P A38 C 6 1555 1555 1.56 LINK O3' A38 C 6 P DG C 7 1555 1555 1.59 LINK O HOH P 103 MG MG A 401 1555 1555 2.12 LINK OD2 ASP A 7 MG MG A 401 1555 1555 2.25 LINK OD1 ASP A 7 MG MG A 402 1555 1555 2.06 LINK O PHE A 8 MG MG A 402 1555 1555 2.15 LINK OD1 ASP A 105 MG MG A 401 1555 1555 1.98 LINK OD2 ASP A 105 MG MG A 402 1555 1555 2.15 LINK OE2 GLU A 106 MG MG A 401 1555 1555 2.46 LINK MG MG A 401 O1A DZ4 A 403 1555 1555 2.51 LINK MG MG A 401 O HOH A 507 1555 1555 2.24 LINK MG MG A 402 O1A DZ4 A 403 1555 1555 2.11 LINK MG MG A 402 O2G DZ4 A 403 1555 1555 2.00 LINK MG MG A 402 O2B DZ4 A 403 1555 1555 2.19 LINK O HOH B 105 MG MG D 401 1555 1555 2.16 LINK OD2 ASP D 7 MG MG D 401 1555 1555 2.24 LINK OD1 ASP D 7 MG MG D 402 1555 1555 2.13 LINK O PHE D 8 MG MG D 402 1555 1555 2.07 LINK OD1 ASP D 105 MG MG D 401 1555 1555 2.13 LINK OD2 ASP D 105 MG MG D 402 1555 1555 2.31 LINK OE2 GLU D 106 MG MG D 401 1555 1555 2.21 LINK MG MG D 401 O1A DZ4 D 403 1555 1555 2.38 LINK MG MG D 401 O HOH D 505 1555 1555 2.67 LINK MG MG D 402 O2B DZ4 D 403 1555 1555 2.20 LINK MG MG D 402 O1A DZ4 D 403 1555 1555 2.13 LINK MG MG D 402 O1G DZ4 D 403 1555 1555 2.11 CISPEP 1 LYS A 159 PRO A 160 0 5.13 CISPEP 2 LYS D 159 PRO D 160 0 2.40 SITE 1 AC1 8 ASP A 7 SER A 103 ASP A 105 GLU A 106 SITE 2 AC1 8 DZ4 A 403 HOH A 507 DG P 13 HOH P 103 SITE 1 AC2 4 ASP A 7 PHE A 8 ASP A 105 DZ4 A 403 SITE 1 AC3 23 ASP A 7 PHE A 8 ASP A 9 TYR A 10 SITE 2 AC3 23 PHE A 11 TYR A 12 ALA A 44 THR A 45 SITE 3 AC3 23 TYR A 48 ARG A 51 ASP A 105 LYS A 159 SITE 4 AC3 23 MG A 401 MG A 402 HOH A 507 HOH A 510 SITE 5 AC3 23 HOH A 512 HOH A 514 DG P 13 HOH P 101 SITE 6 AC3 23 HOH P 105 DT T 5 A38 T 6 SITE 1 AC4 7 DG B 13 HOH B 105 ASP D 7 ASP D 105 SITE 2 AC4 7 GLU D 106 DZ4 D 403 HOH D 505 SITE 1 AC5 4 ASP D 7 PHE D 8 ASP D 105 DZ4 D 403 SITE 1 AC6 22 DG B 13 HOH B 102 HOH B 105 DT C 5 SITE 2 AC6 22 A38 C 6 ASP D 7 PHE D 8 ASP D 9 SITE 3 AC6 22 TYR D 10 PHE D 11 TYR D 12 ALA D 44 SITE 4 AC6 22 THR D 45 TYR D 48 ARG D 51 ASP D 105 SITE 5 AC6 22 LYS D 159 MG D 401 MG D 402 HOH D 504 SITE 6 AC6 22 HOH D 507 HOH D 511 SITE 1 AC7 9 DA C 4 DG C 7 VAL D 32 ALA D 42 SITE 2 AC7 9 ILE D 248 THR D 250 ARG D 331 ARG D 332 SITE 3 AC7 9 DZ4 D 403 SITE 1 AC8 9 DC B 12 DT C 5 DA C 8 ARG D 247 SITE 2 AC8 9 ILE D 248 THR D 250 ARG D 332 ARG D 336 SITE 3 AC8 9 DZ4 D 403 CRYST1 53.098 103.690 99.105 90.00 89.94 90.00 P 1 21 1 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 0.018833 0.000000 -0.000020 0.00000 SCALE2 0.000000 0.009644 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010090 0.00000