PDB Short entry for 4QW9 HEADER TRANSFERASE/DNA 16-JUL-14 4QW9 TITLE TERNARY CRYSTAL STRUCTURES OF A Y-FAMILY DNA POLYMERASE DPO4 FROM TITLE 2 SULFOLOBUS SOLFATARICUS IN COMPLEX WITH DNA AND (-)FTC-PPNP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE IV; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DPO4; COMPND 5 SYNONYM: POL IV; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(P*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3'); COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'- COMPND 14 D(P*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3'); COMPND 15 CHAIN: D; COMPND 16 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 EXPRESSION_SYSTEM_PLASMID: PET21B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 OTHER_DETAILS: RANDOM SEQUENCE, CHEMICALLY SYNTHESIZED; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 OTHER_DETAILS: RANDOM SEQUENCE, CHEMICALLY SYNTHESIZED KEYWDS Y-FAMILY DNA POLYMERASE, TRANSFERASE-DNA COMPLEX, DPO4, POLYMERASE EXPDTA X-RAY DIFFRACTION AUTHOR V.GAUR,Z.SUO REVDAT 3 28-FEB-24 4QW9 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 LINK REVDAT 2 17-SEP-14 4QW9 1 JRNL REVDAT 1 27-AUG-14 4QW9 0 JRNL AUTH V.GAUR,R.VYAS,J.D.FOWLER,G.EFTHIMIOPOULOS,J.Y.FENG,Z.SUO JRNL TITL STRUCTURAL AND KINETIC INSIGHTS INTO BINDING AND JRNL TITL 2 INCORPORATION OF L-NUCLEOTIDE ANALOGS BY A Y-FAMILY DNA JRNL TITL 3 POLYMERASE. JRNL REF NUCLEIC ACIDS RES. V. 42 9984 2014 JRNL REFN ISSN 0305-1048 JRNL PMID 25104018 JRNL DOI 10.1093/NAR/GKU709 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 17427 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) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1907 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 942 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 68.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.4230 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.4270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2743 REMARK 3 NUCLEIC ACID ATOMS : 593 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 135 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 96.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.33000 REMARK 3 B22 (A**2) : 1.42000 REMARK 3 B33 (A**2) : -1.75000 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): 0.639 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.311 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3504 ; 0.012 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 3191 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4848 ; 1.528 ; 1.840 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7374 ; 3.512 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 340 ; 1.348 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 121 ;39.923 ;23.636 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 563 ;18.288 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;22.344 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 525 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3408 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 745 ; 0.011 ; 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): 1698 ; 1.462 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2760 ; 2.706 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1806 ; 2.436 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2088 ; 4.278 ; 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 341 REMARK 3 RESIDUE RANGE : A 701 A 704 REMARK 3 RESIDUE RANGE : A 801 A 899 REMARK 3 ORIGIN FOR THE GROUP (A): 26.0340 -15.4152 -11.6127 REMARK 3 T TENSOR REMARK 3 T11: 0.1364 T22: 0.1240 REMARK 3 T33: 0.0902 T12: -0.0340 REMARK 3 T13: 0.0018 T23: -0.0391 REMARK 3 L TENSOR REMARK 3 L11: 1.0650 L22: 0.4873 REMARK 3 L33: 0.5095 L12: 0.4594 REMARK 3 L13: -0.3715 L23: -0.3159 REMARK 3 S TENSOR REMARK 3 S11: 0.0033 S12: 0.2245 S13: -0.0391 REMARK 3 S21: 0.0502 S22: 0.0715 S23: 0.0147 REMARK 3 S31: -0.1054 S32: -0.0136 S33: -0.0747 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 13 REMARK 3 RESIDUE RANGE : C 101 C 117 REMARK 3 ORIGIN FOR THE GROUP (A): 28.4342 -30.2064 -0.2963 REMARK 3 T TENSOR REMARK 3 T11: 0.1058 T22: 0.0464 REMARK 3 T33: 0.1714 T12: -0.0393 REMARK 3 T13: 0.0547 T23: -0.0156 REMARK 3 L TENSOR REMARK 3 L11: 3.2672 L22: 2.8764 REMARK 3 L33: 3.9856 L12: 0.5836 REMARK 3 L13: -0.3755 L23: -2.5573 REMARK 3 S TENSOR REMARK 3 S11: -0.2353 S12: 0.1824 S13: -0.6804 REMARK 3 S21: 0.2131 S22: 0.0674 S23: -0.0578 REMARK 3 S31: -0.4381 S32: 0.1939 S33: 0.1678 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 3 D 18 REMARK 3 RESIDUE RANGE : D 101 D 119 REMARK 3 ORIGIN FOR THE GROUP (A): 32.0814 -27.0504 -1.9102 REMARK 3 T TENSOR REMARK 3 T11: 0.3068 T22: 0.1264 REMARK 3 T33: 0.1510 T12: -0.0026 REMARK 3 T13: 0.0101 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 0.5445 L22: 1.3513 REMARK 3 L33: 0.4534 L12: 0.0085 REMARK 3 L13: 0.3520 L23: 0.5562 REMARK 3 S TENSOR REMARK 3 S11: 0.0597 S12: 0.1274 S13: -0.1365 REMARK 3 S21: -0.2161 S22: -0.0786 S23: 0.2768 REMARK 3 S31: -0.0418 S32: 0.0666 S33: 0.0189 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 4QW9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000086592. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-11 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 : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : .97931 REMARK 200 MONOCHROMATOR : DIAMOND(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20462 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 29.181 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.63500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG 3350, 100MM CALCIUM ACETATE, REMARK 280 2.5% GLYCEROL 0.1M MES, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 48.40000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 48.40000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.95000 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: 4750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 824 LIES ON A SPECIAL POSITION. 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 LEU A 342 REMARK 465 GLU A 343 REMARK 465 HIS A 344 REMARK 465 HIS A 345 REMARK 465 HIS A 346 REMARK 465 HIS A 347 REMARK 465 HIS A 348 REMARK 465 HIS A 349 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 N TYR A 10 O2C 0G4 A 701 1.82 REMARK 500 C3' DC C 13 O2A 0G4 A 701 1.83 REMARK 500 OG1 THR A 45 O HOH A 891 2.08 REMARK 500 NH2 ARG A 332 O HOH A 877 2.08 REMARK 500 OE1 GLU A 127 O HOH A 833 2.11 REMARK 500 O1B 0G4 A 701 O HOH A 850 2.18 REMARK 500 O5' 0G4 A 701 O HOH A 819 2.18 REMARK 500 OD2 ASP A 231 O HOH A 895 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 DT C 12 O3' DC C 13 P -0.125 REMARK 500 DC D 3 P DC D 3 OP3 -0.087 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 36.15 34.77 REMARK 500 PHE A 11 -64.53 -27.07 REMARK 500 SER A 96 140.44 169.98 REMARK 500 ASP A 113 40.69 -109.81 REMARK 500 LYS A 114 -46.17 -136.93 REMARK 500 SER A 145 -174.98 -178.93 REMARK 500 ILE A 163 109.49 177.12 REMARK 500 LEU A 178 133.00 -39.90 REMARK 500 LEU A 194 -75.01 -59.08 REMARK 500 LYS A 195 39.09 -62.54 REMARK 500 ILE A 199 106.75 -24.40 REMARK 500 ARG A 230 0.24 -69.08 REMARK 500 SER A 255 164.34 175.47 REMARK 500 ASP A 277 -117.31 64.93 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 702 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD2 REMARK 620 2 ASP A 105 OD2 84.4 REMARK 620 3 GLU A 106 OE2 65.4 111.2 REMARK 620 4 0G4 A 701 O2A 164.9 81.2 124.5 REMARK 620 5 0G4 A 701 O2B 103.0 82.3 160.1 70.6 REMARK 620 6 HOH A 828 O 77.1 161.5 60.6 117.2 102.1 REMARK 620 7 HOH A 850 O 123.3 143.9 102.1 68.3 69.9 52.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 703 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD1 REMARK 620 2 PHE A 8 O 90.1 REMARK 620 3 ASP A 105 OD2 88.1 123.8 REMARK 620 4 ASP A 105 OD1 111.2 80.2 49.1 REMARK 620 5 0G4 A 701 O3G 89.0 107.5 128.6 158.7 REMARK 620 6 0G4 A 701 O1A 154.1 109.3 94.6 89.5 69.3 REMARK 620 7 0G4 A 701 O2B 91.3 156.8 79.4 120.5 49.4 64.0 REMARK 620 8 0G4 A 701 O2B 83.4 128.3 107.2 149.1 21.8 71.3 29.3 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 704 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 181 O REMARK 620 2 HOH A 820 O 66.8 REMARK 620 3 HOH C 104 O 116.5 75.3 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0G4 A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 704 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4QW8 RELATED DB: PDB REMARK 900 RELATED ID: 4QWA RELATED DB: PDB REMARK 900 RELATED ID: 4QWB RELATED DB: PDB REMARK 900 RELATED ID: 4QWC RELATED DB: PDB REMARK 900 RELATED ID: 4QWD RELATED DB: PDB REMARK 900 RELATED ID: 4QWE RELATED DB: PDB DBREF 4QW9 A 1 341 UNP Q97W02 DPO4_SULSO 1 341 DBREF 4QW9 C 1 13 PDB 4QW9 4QW9 1 13 DBREF 4QW9 D 3 18 PDB 4QW9 4QW9 3 18 SEQADV 4QW9 LEU A 342 UNP Q97W02 EXPRESSION TAG SEQADV 4QW9 GLU A 343 UNP Q97W02 EXPRESSION TAG SEQADV 4QW9 HIS A 344 UNP Q97W02 EXPRESSION TAG SEQADV 4QW9 HIS A 345 UNP Q97W02 EXPRESSION TAG SEQADV 4QW9 HIS A 346 UNP Q97W02 EXPRESSION TAG SEQADV 4QW9 HIS A 347 UNP Q97W02 EXPRESSION TAG SEQADV 4QW9 HIS A 348 UNP Q97W02 EXPRESSION TAG SEQADV 4QW9 HIS A 349 UNP Q97W02 EXPRESSION TAG SEQRES 1 A 349 MET ILE VAL LEU PHE VAL ASP PHE ASP TYR PHE TYR ALA SEQRES 2 A 349 GLN VAL GLU GLU VAL LEU ASN PRO SER LEU LYS GLY LYS SEQRES 3 A 349 PRO VAL VAL VAL CYS VAL PHE SER GLY ARG PHE GLU ASP SEQRES 4 A 349 SER GLY ALA VAL ALA THR ALA ASN TYR GLU ALA ARG LYS SEQRES 5 A 349 PHE GLY VAL LYS ALA GLY ILE PRO ILE VAL GLU ALA LYS SEQRES 6 A 349 LYS ILE LEU PRO ASN ALA VAL TYR LEU PRO MET ARG LYS SEQRES 7 A 349 GLU VAL TYR GLN GLN VAL SER SER ARG ILE MET ASN LEU SEQRES 8 A 349 LEU ARG GLU TYR SER GLU LYS ILE GLU ILE ALA SER ILE SEQRES 9 A 349 ASP GLU ALA TYR LEU ASP ILE SER ASP LYS VAL ARG ASP SEQRES 10 A 349 TYR ARG GLU ALA TYR ASN LEU GLY LEU GLU ILE LYS ASN SEQRES 11 A 349 LYS ILE LEU GLU LYS GLU LYS ILE THR VAL THR VAL GLY SEQRES 12 A 349 ILE SER LYS ASN LYS VAL PHE ALA LYS ILE ALA ALA ASP SEQRES 13 A 349 MET ALA LYS PRO ASN GLY ILE LYS VAL ILE ASP ASP GLU SEQRES 14 A 349 GLU VAL LYS ARG LEU ILE ARG GLU LEU ASP ILE ALA ASP SEQRES 15 A 349 VAL PRO GLY ILE GLY ASN ILE THR ALA GLU LYS LEU LYS SEQRES 16 A 349 LYS LEU GLY ILE ASN LYS LEU VAL ASP THR LEU SER ILE SEQRES 17 A 349 GLU PHE ASP LYS LEU LYS GLY MET ILE GLY GLU ALA LYS SEQRES 18 A 349 ALA LYS TYR LEU ILE SER LEU ALA ARG ASP GLU TYR ASN SEQRES 19 A 349 GLU PRO ILE ARG THR ARG VAL ARG LYS SER ILE GLY ARG SEQRES 20 A 349 ILE VAL THR MET LYS ARG ASN SER ARG ASN LEU GLU GLU SEQRES 21 A 349 ILE LYS PRO TYR LEU PHE ARG ALA ILE GLU GLU SER TYR SEQRES 22 A 349 TYR LYS LEU ASP LYS ARG ILE PRO LYS ALA ILE HIS VAL SEQRES 23 A 349 VAL ALA VAL THR GLU ASP LEU ASP ILE VAL SER ARG GLY SEQRES 24 A 349 ARG THR PHE PRO HIS GLY ILE SER LYS GLU THR ALA TYR SEQRES 25 A 349 SER GLU SER VAL LYS LEU LEU GLN LYS ILE LEU GLU GLU SEQRES 26 A 349 ASP GLU ARG LYS ILE ARG ARG ILE GLY VAL ARG PHE SER SEQRES 27 A 349 LYS PHE ILE LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 C 13 DG DG DC DT DA DC DA DG DG DA DC DT DC SEQRES 1 D 16 DC DA DG DG DA DG DT DC DC DT DG DT DA SEQRES 2 D 16 DG DC DC HET 0G4 A 701 56 HET CA A 702 1 HET CA A 703 1 HET CA A 704 1 HETNAM 0G4 [[[[(2R,5S)-5-(4-AZANYL-5-FLUORANYL-2-OXIDANYLIDENE- HETNAM 2 0G4 PYRIMIDIN-1-YL)-1,3-OXATHIOLAN-2-YL]METHOXY-OXIDANYL- HETNAM 3 0G4 PHOSPHORYL]OXY -OXIDANYL-PHOSPHORYL]AMINO]PHOSPHONIC HETNAM 4 0G4 ACID HETNAM CA CALCIUM ION HETSYN 0G4 DCTP ANALOG FORMUL 4 0G4 C8 H14 F N4 O11 P3 S FORMUL 5 CA 3(CA 2+) FORMUL 8 HOH *135(H2 O) HELIX 1 1 TYR A 10 ASN A 20 1 11 HELIX 2 2 PRO A 21 LYS A 24 5 4 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 195 1 9 HELIX 11 11 VAL A 203 ILE A 208 1 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 ILE A 101 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 OD2 ASP A 7 CA CA A 702 1555 1555 2.54 LINK OD1 ASP A 7 CA CA A 703 1555 1555 2.20 LINK O PHE A 8 CA CA A 703 1555 1555 2.13 LINK OD2 ASP A 105 CA CA A 702 1555 1555 2.52 LINK OD2 ASP A 105 CA CA A 703 1555 1555 2.61 LINK OD1 ASP A 105 CA CA A 703 1555 1555 2.75 LINK OE2 GLU A 106 CA CA A 702 1555 1555 2.59 LINK O ALA A 181 CA CA A 704 1555 1555 2.60 LINK O2AB0G4 A 701 CA CA A 702 1555 1555 2.41 LINK O2BA0G4 A 701 CA CA A 702 1555 1555 2.49 LINK O3GA0G4 A 701 CA CA A 703 1555 1555 2.03 LINK O1AA0G4 A 701 CA CA A 703 1555 1555 2.12 LINK O2BA0G4 A 701 CA CA A 703 1555 1555 2.55 LINK O2BB0G4 A 701 CA CA A 703 1555 1555 2.68 LINK CA CA A 702 O HOH A 828 1555 1555 2.73 LINK CA CA A 702 O HOH A 850 1555 1555 3.03 LINK CA CA A 704 O HOH A 820 1555 1555 2.84 LINK CA CA A 704 O HOH C 104 1555 1555 2.84 CISPEP 1 LYS A 159 PRO A 160 0 0.13 SITE 1 AC1 24 ASP A 7 PHE A 8 ASP A 9 TYR A 10 SITE 2 AC1 24 PHE A 11 TYR A 12 ALA A 44 THR A 45 SITE 3 AC1 24 ARG A 51 ALA A 57 ASP A 105 LYS A 159 SITE 4 AC1 24 CA A 702 CA A 703 HOH A 818 HOH A 819 SITE 5 AC1 24 HOH A 831 HOH A 845 HOH A 850 HOH A 871 SITE 6 AC1 24 HOH A 891 DC C 13 DG D 5 DG D 6 SITE 1 AC2 8 ASP A 7 ASP A 105 GLU A 106 0G4 A 701 SITE 2 AC2 8 CA A 703 HOH A 828 HOH A 850 DC C 13 SITE 1 AC3 5 ASP A 7 PHE A 8 ASP A 105 0G4 A 701 SITE 2 AC3 5 CA A 702 SITE 1 AC4 4 ALA A 181 ILE A 186 HOH A 820 HOH C 104 CRYST1 96.800 101.900 52.540 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 0.010331 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009814 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019033 0.00000