HEADER TRANSFERASE/DNA 25-MAR-13 4JUZ TITLE TERNARY COMPLEX OF GAMMA-OHPDG ADDUCT MODIFIED DNA (ZERO PRIMER) WITH TITLE 2 DNA POLYMERASE IV AND INCOMING DGTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE IV; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POL IV; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(P*CP*(KAG) COMPND 9 P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*C)-3'); COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 3 ORGANISM_TAXID: 273057; SOURCE 4 STRAIN: ATCC 35092 / DSM 1617 / JCM 11322 / P2; SOURCE 5 GENE: DBH, DPO4, SSO2448; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES KEYWDS TERNARY COMPLEX OF DPO4-DNA-DATP, DNA POLYMERASE, DNA ADDUCT, KEYWDS 2 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.BANERJEE,G.SHANMUGAM,M.P.STONE REVDAT 3 28-FEB-24 4JUZ 1 REMARK SEQADV LINK REVDAT 2 09-OCT-13 4JUZ 1 JRNL REVDAT 1 28-AUG-13 4JUZ 0 JRNL AUTH G.SHANMUGAM,I.G.MINKO,S.BANERJEE,P.P.CHRISTOV,I.D.KOZEKOV, JRNL AUTH 2 C.J.RIZZO,R.S.LLOYD,M.EGLI,M.P.STONE JRNL TITL RING-OPENING OF THE GAMMA-OH-PDG ADDUCT PROMOTES ERROR-FREE JRNL TITL 2 BYPASS BY THE SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4. JRNL REF CHEM.RES.TOXICOL. V. 26 1348 2013 JRNL REFN ISSN 0893-228X JRNL PMID 23947567 JRNL DOI 10.1021/TX400200B REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.2_869 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) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 15480 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1547 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 42.0455 - 5.8946 0.99 1367 153 0.1927 0.2404 REMARK 3 2 5.8946 - 4.6807 1.00 1318 146 0.1750 0.2205 REMARK 3 3 4.6807 - 4.0896 1.00 1295 144 0.1464 0.2335 REMARK 3 4 4.0896 - 3.7159 1.00 1275 142 0.1892 0.2386 REMARK 3 5 3.7159 - 3.4497 1.00 1284 142 0.2098 0.2727 REMARK 3 6 3.4497 - 3.2464 1.00 1275 141 0.2161 0.2783 REMARK 3 7 3.2464 - 3.0839 1.00 1248 138 0.2241 0.3059 REMARK 3 8 3.0839 - 2.9496 1.00 1282 142 0.2644 0.3660 REMARK 3 9 2.9496 - 2.8361 0.99 1243 139 0.3058 0.3960 REMARK 3 10 2.8361 - 2.7383 0.98 1233 138 0.3423 0.4225 REMARK 3 11 2.7383 - 2.6527 0.89 1113 122 0.3453 0.4500 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.32 REMARK 3 B_SOL : 38.09 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.780 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.77500 REMARK 3 B22 (A**2) : -0.29690 REMARK 3 B33 (A**2) : -9.47820 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 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 : 0.009 NULL REMARK 3 ANGLE : 1.300 NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 4JUZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000078537. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15480 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.54500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM TRIS HCL, 15% PEG3350, 100MM REMARK 280 CALCIUM DIACETATE, 2.5% GLYCEROL, PH 7.4, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 47.45300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.17900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.45300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.17900 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: 6030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 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 KAG B 5 C1M 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 GLU A 106 O HOH A 1101 1.99 REMARK 500 O HOH B 106 O HOH B 107 2.04 REMARK 500 O HOH A 1107 O HOH A 1119 2.04 REMARK 500 OP2 DG C 23 O HOH C 106 2.04 REMARK 500 O ILE A 2 O HOH A 1121 2.11 REMARK 500 O HOH A 1103 O HOH A 1104 2.11 REMARK 500 NH2 ARG A 36 OD1 ASN A 254 2.13 REMARK 500 N3 DA C 28 O HOH C 101 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 1108 O HOH C 104 3547 2.13 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 DA B 7 O3' DA B 7 C3' -0.056 REMARK 500 DC C 32 C1' DC C 32 N1 0.089 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 B 4 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 KAG B 5 O3' - P - OP2 ANGL. DEV. = -14.0 DEGREES REMARK 500 KAG B 5 O3' - P - OP1 ANGL. DEV. = 24.7 DEGREES REMARK 500 DG B 6 O5' - C5' - C4' ANGL. DEV. = -6.5 DEGREES REMARK 500 DG B 6 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DA B 7 C1' - O4' - C4' ANGL. DEV. = -7.2 DEGREES REMARK 500 DA B 7 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC B 10 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC B 11 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT B 12 N3 - C4 - O4 ANGL. DEV. = 4.4 DEGREES REMARK 500 DT B 12 C5 - C4 - O4 ANGL. DEV. = -4.6 DEGREES REMARK 500 DT B 13 N3 - C4 - O4 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 14 O5' - C5' - C4' ANGL. DEV. = -6.0 DEGREES REMARK 500 DC B 14 C1' - O4' - C4' ANGL. DEV. = -7.4 DEGREES REMARK 500 DC B 15 C1' - O4' - C4' ANGL. DEV. = -6.9 DEGREES REMARK 500 DC B 17 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DC B 17 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG C 22 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 DG C 23 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA C 24 O5' - C5' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 DC C 31 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DC C 32 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DC C 32 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DC C 32 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 DC C 32 O4' - C1' - N1 ANGL. DEV. = 7.2 DEGREES REMARK 500 DC C 32 C6 - N1 - C2 ANGL. DEV. = -2.6 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 49.75 32.59 REMARK 500 ASN A 20 73.51 -159.03 REMARK 500 PRO A 21 -9.19 -57.60 REMARK 500 ARG A 36 -71.48 -55.91 REMARK 500 ARG A 77 77.62 -119.69 REMARK 500 ASP A 113 37.21 -71.84 REMARK 500 LYS A 114 -41.74 -146.65 REMARK 500 SER A 145 -162.65 -168.03 REMARK 500 ASN A 234 40.70 -163.09 REMARK 500 ASP A 277 86.53 31.30 REMARK 500 LEU A 293 25.70 49.97 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 CA A1001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD1 REMARK 620 2 PHE A 8 O 61.4 REMARK 620 3 ASP A 105 OD2 60.4 103.8 REMARK 620 4 DGT A1000 O3B 100.1 104.9 129.4 REMARK 620 5 DGT A1000 O1A 81.0 137.6 69.8 60.9 REMARK 620 6 DGT A1000 O2B 151.7 126.0 128.9 52.3 79.2 REMARK 620 7 HOH A1124 O 49.0 91.5 84.6 54.1 46.8 102.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1002 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1103 O REMARK 620 2 HOH A1104 O 42.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGT A 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JV0 RELATED DB: PDB REMARK 900 RELATED ID: 4JV1 RELATED DB: PDB REMARK 900 RELATED ID: 4JV2 RELATED DB: PDB DBREF 4JUZ A 1 341 UNP Q97W02 DPO4_SULSO 1 341 DBREF 4JUZ B 4 18 PDB 4JUZ 4JUZ 4 18 DBREF 4JUZ C 19 32 PDB 4JUZ 4JUZ 19 32 SEQADV 4JUZ HIS A -5 UNP Q97W02 EXPRESSION TAG SEQADV 4JUZ HIS A -4 UNP Q97W02 EXPRESSION TAG SEQADV 4JUZ HIS A -3 UNP Q97W02 EXPRESSION TAG SEQADV 4JUZ HIS A -2 UNP Q97W02 EXPRESSION TAG SEQADV 4JUZ HIS A -1 UNP Q97W02 EXPRESSION TAG SEQADV 4JUZ HIS A 0 UNP Q97W02 EXPRESSION TAG SEQRES 1 A 347 HIS HIS HIS HIS HIS HIS MET ILE VAL LEU PHE VAL ASP SEQRES 2 A 347 PHE ASP TYR PHE TYR ALA GLN VAL GLU GLU VAL LEU ASN SEQRES 3 A 347 PRO SER LEU LYS GLY LYS PRO VAL VAL VAL CYS VAL PHE SEQRES 4 A 347 SER GLY ARG PHE GLU ASP SER GLY ALA VAL ALA THR ALA SEQRES 5 A 347 ASN TYR GLU ALA ARG LYS PHE GLY VAL LYS ALA GLY ILE SEQRES 6 A 347 PRO ILE VAL GLU ALA LYS LYS ILE LEU PRO ASN ALA VAL SEQRES 7 A 347 TYR LEU PRO MET ARG LYS GLU VAL TYR GLN GLN VAL SER SEQRES 8 A 347 SER ARG ILE MET ASN LEU LEU ARG GLU TYR SER GLU LYS SEQRES 9 A 347 ILE GLU ILE ALA SER ILE ASP GLU ALA TYR LEU ASP ILE SEQRES 10 A 347 SER ASP LYS VAL ARG ASP TYR ARG GLU ALA TYR ASN LEU SEQRES 11 A 347 GLY LEU GLU ILE LYS ASN LYS ILE LEU GLU LYS GLU LYS SEQRES 12 A 347 ILE THR VAL THR VAL GLY ILE SER LYS ASN LYS VAL PHE SEQRES 13 A 347 ALA LYS ILE ALA ALA ASP MET ALA LYS PRO ASN GLY ILE SEQRES 14 A 347 LYS VAL ILE ASP ASP GLU GLU VAL LYS ARG LEU ILE ARG SEQRES 15 A 347 GLU LEU ASP ILE ALA ASP VAL PRO GLY ILE GLY ASN ILE SEQRES 16 A 347 THR ALA GLU LYS LEU LYS LYS LEU GLY ILE ASN LYS LEU SEQRES 17 A 347 VAL ASP THR LEU SER ILE GLU PHE ASP LYS LEU LYS GLY SEQRES 18 A 347 MET ILE GLY GLU ALA LYS ALA LYS TYR LEU ILE SER LEU SEQRES 19 A 347 ALA ARG ASP GLU TYR ASN GLU PRO ILE ARG THR ARG VAL SEQRES 20 A 347 ARG LYS SER ILE GLY ARG ILE VAL THR MET LYS ARG ASN SEQRES 21 A 347 SER ARG ASN LEU GLU GLU ILE LYS PRO TYR LEU PHE ARG SEQRES 22 A 347 ALA ILE GLU GLU SER TYR TYR LYS LEU ASP LYS ARG ILE SEQRES 23 A 347 PRO LYS ALA ILE HIS VAL VAL ALA VAL THR GLU ASP LEU SEQRES 24 A 347 ASP ILE VAL SER ARG GLY ARG THR PHE PRO HIS GLY ILE SEQRES 25 A 347 SER LYS GLU THR ALA TYR SER GLU SER VAL LYS LEU LEU SEQRES 26 A 347 GLN LYS ILE LEU GLU GLU ASP GLU ARG LYS ILE ARG ARG SEQRES 27 A 347 ILE GLY VAL ARG PHE SER LYS PHE ILE SEQRES 1 B 15 DC KAG DG DA DA DT DC DC DT DT DC DC DC SEQRES 2 B 15 DC DC SEQRES 1 C 14 DG DG DG DG DG DA DA DG DG DA DT DT DC SEQRES 2 C 14 DC MODRES 4JUZ KAG B 5 G HET KAG B 5 26 HET DGT A1000 31 HET CA A1001 1 HET CA A1002 1 HETNAM KAG 2'-DEOXY-N-[(1S)-1-METHYL-3-OXOPROPYL]GUANOSINE 5'- HETNAM 2 KAG PHOSPHATE HETNAM DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM CA CALCIUM ION FORMUL 2 KAG C14 H20 N5 O8 P FORMUL 4 DGT C10 H16 N5 O13 P3 FORMUL 5 CA 2(CA 2+) FORMUL 7 HOH *40(H2 O) HELIX 1 1 TYR A 10 LEU A 19 1 10 HELIX 2 2 ASN A 20 LYS A 24 5 5 HELIX 3 3 ASN A 47 LYS A 52 1 6 HELIX 4 4 PRO A 60 LEU A 68 1 9 HELIX 5 5 ARG A 77 GLU A 94 1 18 HELIX 6 6 ASP A 117 LYS A 137 1 21 HELIX 7 7 ASN A 147 LYS A 159 1 13 HELIX 8 8 ASP A 167 LEU A 178 1 12 HELIX 9 9 ASP A 179 VAL A 183 5 5 HELIX 10 10 GLY A 187 LYS A 196 1 10 HELIX 11 11 LEU A 202 SER A 207 5 6 HELIX 12 12 GLU A 209 GLY A 218 1 10 HELIX 13 13 GLY A 218 ARG A 230 1 13 HELIX 14 14 ASN A 257 ASP A 277 1 21 HELIX 15 15 SER A 307 ASP A 326 1 20 SHEET 1 A 5 ILE A 99 SER A 103 0 SHEET 2 A 5 GLU A 106 ASP A 110 -1 O TYR A 108 N GLU A 100 SHEET 3 A 5 VAL A 3 PHE A 8 -1 N VAL A 6 O ALA A 107 SHEET 4 A 5 VAL A 140 SER A 145 -1 O GLY A 143 N PHE A 5 SHEET 5 A 5 ILE A 163 VAL A 165 1 O LYS A 164 N ILE A 144 SHEET 1 B 3 GLY A 41 ALA A 46 0 SHEET 2 B 3 VAL A 28 PHE A 33 -1 N VAL A 32 O ALA A 42 SHEET 3 B 3 VAL A 72 PRO A 75 1 O LEU A 74 N CYS A 31 SHEET 1 C 4 SER A 244 SER A 255 0 SHEET 2 C 4 ILE A 330 PHE A 340 -1 O PHE A 337 N ILE A 245 SHEET 3 C 4 PRO A 281 THR A 290 -1 N VAL A 289 O ARG A 331 SHEET 4 C 4 ILE A 295 THR A 301 -1 O ARG A 298 N VAL A 286 LINK O3' DC B 4 P KAG B 5 1555 1555 1.63 LINK O3' KAG B 5 P DG B 6 1555 1555 1.59 LINK OD1 ASP A 7 CA CA A1001 1555 1555 2.93 LINK O PHE A 8 CA CA A1001 1555 1555 2.59 LINK OD2 ASP A 105 CA CA A1001 1555 1555 2.90 LINK O3B DGT A1000 CA CA A1001 1555 1555 2.90 LINK O1A DGT A1000 CA CA A1001 1555 1555 2.95 LINK O2B DGT A1000 CA CA A1001 1555 1555 3.07 LINK CA CA A1001 O HOH A1124 1555 1555 2.89 LINK CA CA A1002 O HOH A1103 1555 1555 2.90 LINK CA CA A1002 O HOH A1104 1555 1555 2.87 CISPEP 1 LYS A 159 PRO A 160 0 5.67 SITE 1 AC1 18 PHE A 8 ASP A 9 TYR A 10 PHE A 11 SITE 2 AC1 18 TYR A 12 ALA A 44 THR A 45 TYR A 48 SITE 3 AC1 18 ARG A 51 ASP A 105 LYS A 159 CA A1001 SITE 4 AC1 18 HOH A1101 HOH A1120 HOH A1124 DC B 4 SITE 5 AC1 18 KAG B 5 DC C 32 SITE 1 AC2 5 ASP A 7 PHE A 8 ASP A 105 DGT A1000 SITE 2 AC2 5 HOH A1124 SITE 1 AC3 3 ALA A 181 HOH A1103 HOH A1104 CRYST1 94.906 104.358 52.489 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 0.010537 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009582 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019052 0.00000