PDB Short entry for 3GIM HEADER TRANSFERASE/DNA 05-MAR-09 3GIM TITLE DPO4 EXTENSION TERNARY COMPLEX WITH OXOG(ANTI)-G(SYN) PAIR 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: 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(DDG))-3'; COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: PRIMER STRAND (DIDEOXY-TERMINATED AT 3'-END); COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(*CP*TP*AP*AP*CP*(8OG) COMPND 14 P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*C)-3'; COMPND 15 CHAIN: E; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: OXOG-MODIFIED TEMPLATE STRAND SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS P2; SOURCE 3 ORGANISM_TAXID: 273057; SOURCE 4 STRAIN: P2 / DSM 1617 / JCM 11322; SOURCE 5 ATCC: 35092; SOURCE 6 GENE: DBH, DPO4, SSO2448; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-RIL(STRATAGENE); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 OTHER_DETAILS: DNA PRIMER STRAND; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 OTHER_DETAILS: DNA OXOG-MODIFIED TEMPLATE STRAND KEYWDS DNA POLYMERASE, 8-OXOGUANINE, Y-FAMILY, LESION BYPASS, DNA DAMAGE, KEYWDS 2 DNA REPAIR, DNA REPLICATION, DNA-BINDING, DNA-DIRECTED DNA KEYWDS 3 POLYMERASE, MAGNESIUM, METAL-BINDING, MUTATOR PROTEIN, KEYWDS 4 NUCLEOTIDYLTRANSFERASE, TRANSFERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR O.RECHKOBLIT,L.MALININA,D.J.PATEL REVDAT 5 06-SEP-23 3GIM 1 REMARK DBREF SEQADV LINK REVDAT 4 01-NOV-17 3GIM 1 REMARK REVDAT 3 07-DEC-11 3GIM 1 JRNL REVDAT 2 13-JUL-11 3GIM 1 VERSN REVDAT 1 19-MAY-09 3GIM 0 JRNL AUTH O.RECHKOBLIT,L.MALININA,Y.CHENG,N.E.GEACINTOV,S.BROYDE, JRNL AUTH 2 D.J.PATEL JRNL TITL IMPACT OF CONFORMATIONAL HETEROGENEITY OF OXOG LESIONS AND JRNL TITL 2 THEIR PAIRING PARTNERS ON BYPASS FIDELITY BY Y FAMILY JRNL TITL 3 POLYMERASES. JRNL REF STRUCTURE V. 17 725 2009 JRNL REFN ISSN 0969-2126 JRNL PMID 19446528 JRNL DOI 10.1016/J.STR.2009.03.011 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 15879 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) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 797 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 805 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.11 REMARK 3 BIN R VALUE (WORKING SET) : 0.3360 REMARK 3 BIN FREE R VALUE SET COUNT : 51 REMARK 3 BIN FREE R VALUE : 0.4160 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2740 REMARK 3 NUCLEIC ACID ATOMS : 630 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 41 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.92000 REMARK 3 B22 (A**2) : -5.51000 REMARK 3 B33 (A**2) : -3.41000 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): 0.990 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.372 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.319 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 31.854 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3540 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4885 ; 1.522 ; 2.226 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 342 ; 5.212 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 122 ;34.247 ;23.607 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 561 ;18.949 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;16.441 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 556 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2361 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1558 ; 0.265 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2354 ; 0.338 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 228 ; 0.223 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.347 ; 0.500 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 27 ; 0.259 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.255 ; 0.500 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): 1743 ; 0.431 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2766 ; 0.698 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2228 ; 0.917 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2119 ; 1.632 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 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 1 A 341 REMARK 3 ORIGIN FOR THE GROUP (A): 21.7650 18.6730 12.2320 REMARK 3 T TENSOR REMARK 3 T11: -0.2599 T22: -0.0896 REMARK 3 T33: -0.1806 T12: 0.0020 REMARK 3 T13: -0.0113 T23: 0.0437 REMARK 3 L TENSOR REMARK 3 L11: 1.2068 L22: 7.9912 REMARK 3 L33: 5.2602 L12: -0.5772 REMARK 3 L13: 0.1191 L23: -4.3505 REMARK 3 S TENSOR REMARK 3 S11: -0.1452 S12: -0.1159 S13: 0.0567 REMARK 3 S21: 0.4666 S22: 0.4998 S23: 0.5391 REMARK 3 S31: -0.3250 S32: -0.4889 S33: -0.3546 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 802 D 814 REMARK 3 RESIDUE RANGE : E 901 E 918 REMARK 3 RESIDUE RANGE : A 414 A 414 REMARK 3 ORIGIN FOR THE GROUP (A): 11.6660 10.5970 21.0010 REMARK 3 T TENSOR REMARK 3 T11: 0.1121 T22: 0.3945 REMARK 3 T33: 0.2182 T12: 0.0656 REMARK 3 T13: 0.2535 T23: 0.2158 REMARK 3 L TENSOR REMARK 3 L11: 2.7370 L22: 4.1908 REMARK 3 L33: 2.4317 L12: 0.6437 REMARK 3 L13: 1.0631 L23: -1.4223 REMARK 3 S TENSOR REMARK 3 S11: 0.1534 S12: -0.7051 S13: 0.3594 REMARK 3 S21: 1.0439 S22: 0.6293 S23: 1.3370 REMARK 3 S31: 0.0628 S32: -1.1194 S33: -0.7827 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3GIM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000051906. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : 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) : 0.97911 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : 6144 X 6144 PIXEL ELEMENTS WITH REMARK 200 AN EFFECTIVE PIXEL SIZE LESS REMARK 200 THAN 60X60 MICRON AND RESOLUTION REMARK 200 OF ORDER 90X90 MICRON REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15930 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.5800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.49300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 3GIK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, 100 MM CALCIUM ACETATE, REMARK 280 10% PEG 4000, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 49.83400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.96200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 49.83400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.96200 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: 4020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, E 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 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 HIS A 304 O - C - N ANGL. DEV. = -13.2 DEGREES REMARK 500 DT D 803 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT D 804 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DT D 804 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG D 805 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 DG D 805 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG D 810 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG D 813 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA E 903 O4' - C4' - C3' ANGL. DEV. = -2.4 DEGREES REMARK 500 DC E 914 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC E 915 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA E 917 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR A 10 68.41 21.46 REMARK 500 PRO A 21 -1.08 -52.53 REMARK 500 ASP A 39 5.84 89.02 REMARK 500 THR A 45 164.09 171.58 REMARK 500 LEU A 68 57.63 -142.28 REMARK 500 ARG A 77 68.38 -112.96 REMARK 500 GLU A 136 2.14 -165.09 REMARK 500 LYS A 137 25.21 48.83 REMARK 500 SER A 145 -168.10 -163.34 REMARK 500 ILE A 163 119.33 -167.37 REMARK 500 ASP A 168 -33.63 -37.80 REMARK 500 ILE A 175 -17.69 -45.81 REMARK 500 ALA A 191 8.28 -65.42 REMARK 500 ASP A 211 -52.55 -26.55 REMARK 500 ASN A 234 83.95 -155.85 REMARK 500 ASP A 277 113.75 23.35 REMARK 500 LYS A 278 -43.65 81.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 HIS A 304 13.31 REMARK 500 HIS A 304 19.79 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 A 415 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD1 REMARK 620 2 ASP A 7 OD2 53.4 REMARK 620 3 ASP A 105 OD1 70.6 122.0 REMARK 620 4 GLU A 106 OE2 102.5 75.7 105.6 REMARK 620 5 DGT A 414 O2A 85.5 100.5 88.1 165.7 REMARK 620 6 HOH D 373 O 121.3 72.4 164.6 82.1 83.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 416 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD1 REMARK 620 2 PHE A 8 O 86.9 REMARK 620 3 ASP A 105 OD2 66.7 77.3 REMARK 620 4 DGT A 414 O1G 127.2 111.9 162.3 REMARK 620 5 DGT A 414 O1B 152.4 89.8 85.9 79.2 REMARK 620 6 DGT A 414 O2A 90.6 161.0 84.4 84.5 83.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 417 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 181 O REMARK 620 2 ILE A 186 O 97.8 REMARK 620 3 HOH A 342 O 84.2 62.1 REMARK 620 4 HOH A 346 O 105.3 95.7 157.2 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 DGT A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 417 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ASD RELATED DB: PDB REMARK 900 OXOG-MODIFIED DPO4 INSERTION TERNARY COMPLEX REMARK 900 RELATED ID: 2ASJ RELATED DB: PDB REMARK 900 OXOG-MODIFIED DPO4 PRE-INSERTION BINARY COMPLEX REMARK 900 RELATED ID: 2ASL RELATED DB: PDB REMARK 900 OXOG-MODIFIED DPO4 POST-INSERTION BINARY COMPLEX REMARK 900 RELATED ID: 3GII RELATED DB: PDB REMARK 900 DPO4 EXTENSION TERNARY COMPLEX WITH DISORDERED A OPPOSITE AN OXOG REMARK 900 IN ANTI CONFORMATION REMARK 900 RELATED ID: 3GIJ RELATED DB: PDB REMARK 900 DPO4 EXTENSION TERNARY COMPLEX WITH OXOG(SYN)-A(ANTI) AND OXOG(ANTI) REMARK 900 -A(SYN) PAIRS REMARK 900 RELATED ID: 3GIK RELATED DB: PDB REMARK 900 DPO4 EXTENSION TERNARY COMPLEX WITH THE OXOG(ANTI)-C(ANTI) PAIR REMARK 900 RELATED ID: 3GIL RELATED DB: PDB REMARK 900 DPO4 EXTENSION TERNARY COMPLEX WITH OXOG(ANTI)-T(ANTI) PAIR DBREF 3GIM A 2 341 UNP Q97W02 DPO42_SULSO 2 341 DBREF 3GIM D 802 814 PDB 3GIM 3GIM 802 814 DBREF 3GIM E 901 918 PDB 3GIM 3GIM 901 918 SEQADV 3GIM GLY A 1 UNP Q97W02 EXPRESSION TAG SEQRES 1 A 341 GLY 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 D 13 DG DT DT DG DG DA DT DG DG DT DA DG DDG SEQRES 1 E 18 DC DT DA DA DC 8OG DC DT DA DC DC DA DT SEQRES 2 E 18 DC DC DA DA DC MODRES 3GIM DDG D 814 DG MODRES 3GIM 8OG E 906 DG HET DDG D 814 21 HET 8OG E 906 23 HET DGT A 414 31 HET CA A 415 1 HET CA A 416 1 HET CA A 417 1 HETNAM DDG 2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM CA CALCIUM ION HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 2 DDG C10 H14 N5 O6 P FORMUL 3 8OG C10 H14 N5 O8 P FORMUL 4 DGT C10 H16 N5 O13 P3 FORMUL 5 CA 3(CA 2+) FORMUL 8 HOH *41(H2 O) HELIX 1 1 TYR A 10 ASN A 20 1 11 HELIX 2 2 ASN A 47 PHE A 53 1 7 HELIX 3 3 PRO A 60 LEU A 68 1 9 HELIX 4 4 ARG A 77 SER A 96 1 20 HELIX 5 5 ASP A 117 LYS A 137 1 21 HELIX 6 6 ASN A 147 LYS A 159 1 13 HELIX 7 7 ASP A 167 LEU A 178 1 12 HELIX 8 8 ASP A 179 VAL A 183 5 5 HELIX 9 9 LYS A 201 LEU A 206 5 6 HELIX 10 10 GLU A 209 GLY A 218 1 10 HELIX 11 11 GLY A 218 ARG A 230 1 13 HELIX 12 12 ASN A 257 ASP A 277 1 21 HELIX 13 13 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 LEU A 4 O LEU A 109 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 30 O ALA A 44 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 VAL A 335 N ARG A 247 SHEET 3 C 4 PRO A 281 THR A 290 -1 N VAL A 289 O ARG A 332 SHEET 4 C 4 ILE A 295 THR A 301 -1 O VAL A 296 N ALA A 288 LINK O3' DG D 813 P DDG D 814 1555 1555 1.61 LINK O3' DC E 905 P 8OG E 906 1555 1555 1.62 LINK O3' 8OG E 906 P DC E 907 1555 1555 1.60 LINK OD1 ASP A 7 CA CA A 415 1555 1555 2.53 LINK OD2 ASP A 7 CA CA A 415 1555 1555 2.34 LINK OD1 ASP A 7 CA CA A 416 1555 1555 2.31 LINK O PHE A 8 CA CA A 416 1555 1555 2.30 LINK OD1 ASP A 105 CA CA A 415 1555 1555 2.33 LINK OD2 ASP A 105 CA CA A 416 1555 1555 2.34 LINK OE2 GLU A 106 CA CA A 415 1555 1555 2.35 LINK O ALA A 181 CA CA A 417 1555 1555 2.32 LINK O ILE A 186 CA CA A 417 1555 1555 2.32 LINK O HOH A 342 CA CA A 417 1555 1555 2.07 LINK O HOH A 346 CA CA A 417 1555 1555 2.86 LINK O2A DGT A 414 CA CA A 415 1555 1555 2.32 LINK O1G DGT A 414 CA CA A 416 1555 1555 2.34 LINK O1B DGT A 414 CA CA A 416 1555 1555 2.32 LINK O2A DGT A 414 CA CA A 416 1555 1555 2.32 LINK CA CA A 415 O HOH D 373 1555 1555 2.56 CISPEP 1 LYS A 159 PRO A 160 0 -2.93 SITE 1 AC1 18 ASP A 7 PHE A 8 TYR A 10 PHE A 11 SITE 2 AC1 18 TYR A 12 VAL A 32 ALA A 44 THR A 45 SITE 3 AC1 18 TYR A 48 ARG A 51 ASP A 105 LYS A 159 SITE 4 AC1 18 HOH A 375 CA A 415 CA A 416 DDG D 814 SITE 5 AC1 18 DC E 905 8OG E 906 SITE 1 AC2 7 ASP A 7 ASP A 105 GLU A 106 DGT A 414 SITE 2 AC2 7 CA A 416 HOH D 373 DDG D 814 SITE 1 AC3 6 ASP A 7 PHE A 8 ASP A 105 LYS A 159 SITE 2 AC3 6 DGT A 414 CA A 415 SITE 1 AC4 4 ALA A 181 ILE A 186 HOH A 342 HOH A 346 CRYST1 99.668 111.924 53.158 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 0.010033 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008935 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018812 0.00000