HEADER TRANSFERASE/DNA 16-JUL-14 4QW8 TITLE TERNARY CRYSTAL STRUCTURES OF A Y-FAMILY DNA POLYMERASE DPO4 FROM TITLE 2 SULFOLOBUS SOLFATARICUS IN COMPLEX WITH DNA AND D-DCTP 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 OTHER_DETAILS: GGCTACAGGACTC; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'- COMPND 15 D(P*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3'); COMPND 16 CHAIN: D; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: CAGGAGTCCTGTAGCC 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 EXPDTA X-RAY DIFFRACTION AUTHOR V.GAUR,Z.SUO REVDAT 3 28-FEB-24 4QW8 1 REMARK SEQADV LINK REVDAT 2 17-SEP-14 4QW8 1 JRNL REVDAT 1 27-AUG-14 4QW8 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. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 21603 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) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1167 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) : 2.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.35 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1367 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.3040 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.3460 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 : 242 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.37000 REMARK 3 B22 (A**2) : 1.20000 REMARK 3 B33 (A**2) : -0.83000 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): 0.363 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.229 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.155 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.415 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3475 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4803 ; 1.522 ; 2.216 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 340 ; 2.704 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 121 ;38.753 ;23.636 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 563 ;15.749 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;16.096 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 549 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2326 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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 ; 1.410 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2760 ; 2.605 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1777 ; 2.627 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2043 ; 4.173 ; 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): 3480 ; 2.728 ; 3.000 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 341 REMARK 3 RESIDUE RANGE : A 702 A 704 REMARK 3 ORIGIN FOR THE GROUP (A): -26.4665 15.4598 -11.5017 REMARK 3 T TENSOR REMARK 3 T11: 0.0466 T22: 0.0461 REMARK 3 T33: 0.0153 T12: 0.0064 REMARK 3 T13: -0.0070 T23: 0.0134 REMARK 3 L TENSOR REMARK 3 L11: 1.4849 L22: 0.3634 REMARK 3 L33: 0.5431 L12: 0.4051 REMARK 3 L13: 0.4469 L23: 0.2612 REMARK 3 S TENSOR REMARK 3 S11: 0.0259 S12: 0.2396 S13: 0.0332 REMARK 3 S21: 0.0582 S22: 0.0407 S23: -0.0101 REMARK 3 S31: 0.0680 S32: 0.0312 S33: -0.0666 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 : D 3 D 18 REMARK 3 ORIGIN FOR THE GROUP (A): -30.7914 28.3628 -1.1941 REMARK 3 T TENSOR REMARK 3 T11: 0.1071 T22: 0.0724 REMARK 3 T33: 0.1821 T12: -0.0189 REMARK 3 T13: 0.0065 T23: -0.0172 REMARK 3 L TENSOR REMARK 3 L11: 0.6702 L22: 1.9420 REMARK 3 L33: 0.7701 L12: -0.1197 REMARK 3 L13: 0.1839 L23: 0.9205 REMARK 3 S TENSOR REMARK 3 S11: 0.0940 S12: 0.0454 S13: 0.2414 REMARK 3 S21: 0.0351 S22: -0.1980 S23: -0.2330 REMARK 3 S31: 0.0707 S32: -0.1934 S33: 0.1040 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 801 A 976 REMARK 3 RESIDUE RANGE : C 101 C 125 REMARK 3 RESIDUE RANGE : D 101 D 141 REMARK 3 ORIGIN FOR THE GROUP (A): -26.1547 18.9578 -9.8947 REMARK 3 T TENSOR REMARK 3 T11: 0.1247 T22: 0.0793 REMARK 3 T33: 0.0453 T12: -0.0132 REMARK 3 T13: 0.0160 T23: 0.0241 REMARK 3 L TENSOR REMARK 3 L11: 0.7452 L22: 0.1790 REMARK 3 L33: 0.2140 L12: 0.2399 REMARK 3 L13: 0.3826 L23: 0.1144 REMARK 3 S TENSOR REMARK 3 S11: -0.0321 S12: 0.1181 S13: 0.0302 REMARK 3 S21: 0.0467 S22: 0.0443 S23: 0.0265 REMARK 3 S31: -0.0124 S32: 0.0387 S33: -0.0123 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 701 A 701 REMARK 3 ORIGIN FOR THE GROUP (A): -27.3992 11.1538 -17.8745 REMARK 3 T TENSOR REMARK 3 T11: 0.0614 T22: 0.0299 REMARK 3 T33: 0.0358 T12: 0.0282 REMARK 3 T13: -0.0313 T23: -0.0079 REMARK 3 L TENSOR REMARK 3 L11: 25.7262 L22: 2.8487 REMARK 3 L33: 29.2300 L12: 0.6691 REMARK 3 L13: -15.5487 L23: 7.0889 REMARK 3 S TENSOR REMARK 3 S11: 0.0502 S12: 0.6629 S13: 0.3502 REMARK 3 S21: -0.0038 S22: 0.0170 S23: 0.0779 REMARK 3 S31: -0.0612 S32: -0.3087 S33: -0.0672 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 4QW8 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_1000086591. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 120 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 : 23801 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.290 REMARK 200 RESOLUTION RANGE LOW (A) : 19.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.12700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 9.50 REMARK 200 R MERGE FOR SHELL (I) : 0.92200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.500 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 (%): 54.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 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 49.03650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.15850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 49.03650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.15850 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: 5510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 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 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 O ASN A 47 O HOH A 966 1.77 REMARK 500 O LYS A 193 O HOH A 946 1.94 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 948 O HOH D 126 4554 2.11 REMARK 500 O HOH A 967 O HOH D 130 3445 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DC D 3 P DC D 3 OP3 -0.095 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 DA D 4 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC D 18 O4' - C1' - N1 ANGL. DEV. = 3.0 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 48.09 27.52 REMARK 500 ASP A 39 2.05 85.42 REMARK 500 SER A 96 133.49 176.92 REMARK 500 ASP A 117 -159.34 -134.04 REMARK 500 SER A 145 -166.79 -167.34 REMARK 500 ASN A 161 46.93 34.38 REMARK 500 LYS A 196 -4.74 -150.31 REMARK 500 ASP A 277 -117.63 59.97 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 A 702 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD2 REMARK 620 2 GLU A 106 OE2 99.3 REMARK 620 3 HOH A 801 O 95.1 93.9 REMARK 620 4 HOH A 908 O 98.0 162.3 80.8 REMARK 620 5 DC C 13 OP1 153.3 84.7 111.1 81.6 REMARK 620 6 HOH C 125 O 87.2 91.9 173.4 92.8 66.2 REMARK 620 N 1 2 3 4 5 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 92.4 REMARK 620 3 ASP A 105 OD1 90.2 89.4 REMARK 620 4 DCP A 701 O2B 172.0 90.4 97.3 REMARK 620 5 DCP A 701 O1A 109.3 158.1 92.9 67.8 REMARK 620 6 DCP A 701 O2G 104.4 101.5 161.2 67.7 71.4 REMARK 620 N 1 2 3 4 5 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 ILE A 186 O 67.2 REMARK 620 3 HOH A 817 O 68.6 64.5 REMARK 620 4 HOH A 937 O 74.8 53.3 116.0 REMARK 620 5 HOH C 104 O 138.3 71.6 88.3 86.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCP 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: 4QW9 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 4QW8 A 1 341 UNP Q97W02 DPO4_SULSO 1 341 DBREF 4QW8 C 1 13 PDB 4QW8 4QW8 1 13 DBREF 4QW8 D 3 18 PDB 4QW8 4QW8 3 18 SEQADV 4QW8 LEU A 342 UNP Q97W02 EXPRESSION TAG SEQADV 4QW8 GLU A 343 UNP Q97W02 EXPRESSION TAG SEQADV 4QW8 HIS A 344 UNP Q97W02 EXPRESSION TAG SEQADV 4QW8 HIS A 345 UNP Q97W02 EXPRESSION TAG SEQADV 4QW8 HIS A 346 UNP Q97W02 EXPRESSION TAG SEQADV 4QW8 HIS A 347 UNP Q97W02 EXPRESSION TAG SEQADV 4QW8 HIS A 348 UNP Q97W02 EXPRESSION TAG SEQADV 4QW8 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 DCP A 701 28 HET CA A 702 1 HET CA A 703 1 HET CA A 704 1 HETNAM DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE HETNAM CA CALCIUM ION FORMUL 4 DCP C9 H16 N3 O13 P3 FORMUL 5 CA 3(CA 2+) FORMUL 8 HOH *242(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 ARG A 93 1 17 HELIX 6 6 GLU A 94 SER A 96 5 3 HELIX 7 7 ASP A 117 LYS A 137 1 21 HELIX 8 8 ASN A 147 ASP A 156 1 10 HELIX 9 9 ASP A 167 LEU A 178 1 12 HELIX 10 10 ASP A 179 VAL A 183 5 5 HELIX 11 11 GLY A 187 LYS A 195 1 9 HELIX 12 12 LEU A 202 LEU A 206 5 5 HELIX 13 13 GLU A 209 GLY A 218 1 10 HELIX 14 14 GLY A 218 ARG A 230 1 13 HELIX 15 15 ASN A 257 ASP A 277 1 21 HELIX 16 16 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 VAL A 142 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 ILE A 330 N SER A 255 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 VAL A 296 N ALA A 288 LINK OD2 ASP A 7 CA CA A 702 1555 1555 2.57 LINK OD1 ASP A 7 CA CA A 703 1555 1555 2.40 LINK O PHE A 8 CA CA A 703 1555 1555 2.39 LINK OD1 ASP A 105 CA CA A 703 1555 1555 2.37 LINK OE2 GLU A 106 CA CA A 702 1555 1555 2.49 LINK O ALA A 181 CA CA A 704 1555 1555 2.60 LINK O ILE A 186 CA CA A 704 1555 1555 3.18 LINK O2B DCP A 701 CA CA A 703 1555 1555 2.29 LINK O1A DCP A 701 CA CA A 703 1555 1555 2.43 LINK O2G DCP A 701 CA CA A 703 1555 1555 2.47 LINK CA CA A 702 O HOH A 801 1555 1555 2.55 LINK CA CA A 702 O HOH A 908 1555 1555 2.61 LINK CA CA A 702 OP1 DC C 13 1555 1555 2.64 LINK CA CA A 702 O HOH C 125 1555 1555 2.75 LINK CA CA A 704 O HOH A 817 1555 1555 2.78 LINK CA CA A 704 O HOH A 937 1555 1555 2.81 LINK CA CA A 704 O HOH C 104 1555 1555 2.78 CISPEP 1 LYS A 159 PRO A 160 0 -0.92 SITE 1 AC1 19 PHE A 8 ASP A 9 TYR A 10 PHE A 11 SITE 2 AC1 19 TYR A 12 ALA A 44 THR A 45 ARG A 51 SITE 3 AC1 19 ASP A 105 LYS A 159 CA A 703 HOH A 801 SITE 4 AC1 19 HOH A 802 HOH A 803 HOH A 834 HOH A 908 SITE 5 AC1 19 HOH A 970 DC C 13 DG D 5 SITE 1 AC2 6 ASP A 7 GLU A 106 HOH A 801 HOH A 908 SITE 2 AC2 6 DC C 13 HOH C 125 SITE 1 AC3 4 ASP A 7 PHE A 8 ASP A 105 DCP A 701 SITE 1 AC4 5 ALA A 181 ILE A 186 HOH A 817 HOH A 937 SITE 2 AC4 5 HOH C 104 CRYST1 98.073 102.317 52.495 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 0.010196 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009774 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019049 0.00000