PDB Short entry for 3PR4 HEADER TRANSFERASE/DNA 29-NOV-10 3PR4 TITLE DPO4 Y12A MUTANT INCORPORATING DADP OPPOSITE TEMPLATE DT 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 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*C)-3'); COMPND 10 CHAIN: P; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'- COMPND 14 D(*TP*TP*CP*AP*TP*GP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'); COMPND 15 CHAIN: T; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 3 ORGANISM_TAXID: 2287; SOURCE 4 GENE: DBH, DPO4, SSO2448; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES KEYWDS DNA POLYMERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.N.KIROUAC,Z.SUO,H.LING REVDAT 3 06-SEP-23 3PR4 1 REMARK SEQADV LINK REVDAT 2 23-MAR-11 3PR4 1 JRNL REVDAT 1 23-FEB-11 3PR4 0 JRNL AUTH K.N.KIROUAC,Z.SUO,H.LING JRNL TITL STRUCTURAL MECHANISM OF RIBONUCLEOTIDE DISCRIMINATION BY A JRNL TITL 2 Y-FAMILY DNA POLYMERASE. JRNL REF J.MOL.BIOL. V. 407 382 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21295588 JRNL DOI 10.1016/J.JMB.2011.01.037 REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 26.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 15419 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 793 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 26.1143 - 4.8071 0.97 2511 146 0.1753 0.2133 REMARK 3 2 4.8071 - 3.8193 1.00 2461 126 0.1538 0.2056 REMARK 3 3 3.8193 - 3.3377 1.00 2440 131 0.1960 0.2683 REMARK 3 4 3.3377 - 3.0330 1.00 2449 115 0.2225 0.3009 REMARK 3 5 3.0330 - 2.8159 0.99 2392 129 0.2875 0.3531 REMARK 3 6 2.8159 - 2.6500 0.99 2373 146 0.3352 0.4163 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 : 0.95 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 51.21 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.92750 REMARK 3 B22 (A**2) : 1.13280 REMARK 3 B33 (A**2) : 0.79470 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 3359 REMARK 3 ANGLE : 1.291 4656 REMARK 3 CHIRALITY : 0.067 541 REMARK 3 PLANARITY : 0.005 489 REMARK 3 DIHEDRAL : 20.420 1306 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 1:91) REMARK 3 ORIGIN FOR THE GROUP (A): 30.2929 5.3988 19.7970 REMARK 3 T TENSOR REMARK 3 T11: 0.2880 T22: 0.3159 REMARK 3 T33: 0.2103 T12: 0.0263 REMARK 3 T13: -0.0115 T23: 0.0220 REMARK 3 L TENSOR REMARK 3 L11: 0.5361 L22: 1.1616 REMARK 3 L33: 0.8555 L12: -0.6807 REMARK 3 L13: 0.6915 L23: -0.0004 REMARK 3 S TENSOR REMARK 3 S11: -0.0176 S12: -0.1602 S13: -0.1762 REMARK 3 S21: -0.0386 S22: 0.1372 S23: 0.0389 REMARK 3 S31: -0.0395 S32: 0.1811 S33: -0.0541 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 92:219) REMARK 3 ORIGIN FOR THE GROUP (A): 12.7629 19.5234 17.7412 REMARK 3 T TENSOR REMARK 3 T11: 0.2062 T22: 0.3272 REMARK 3 T33: 0.2198 T12: 0.0131 REMARK 3 T13: 0.0096 T23: -0.0455 REMARK 3 L TENSOR REMARK 3 L11: 2.0201 L22: 1.7636 REMARK 3 L33: 0.4160 L12: -1.0540 REMARK 3 L13: -0.1604 L23: 0.0144 REMARK 3 S TENSOR REMARK 3 S11: -0.2830 S12: -0.5215 S13: 0.0634 REMARK 3 S21: 0.0185 S22: 0.3335 S23: 0.1405 REMARK 3 S31: 0.0535 S32: -0.0071 S33: -0.0407 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 220:239) REMARK 3 ORIGIN FOR THE GROUP (A): 11.6178 28.9494 10.4394 REMARK 3 T TENSOR REMARK 3 T11: 0.3924 T22: 0.4136 REMARK 3 T33: 0.3747 T12: 0.0140 REMARK 3 T13: -0.1060 T23: -0.0727 REMARK 3 L TENSOR REMARK 3 L11: 0.7084 L22: 1.4581 REMARK 3 L33: 0.5613 L12: 0.5820 REMARK 3 L13: 0.4083 L23: -0.1879 REMARK 3 S TENSOR REMARK 3 S11: -0.0225 S12: -0.2683 S13: 0.0956 REMARK 3 S21: -0.4806 S22: -0.1214 S23: -0.0323 REMARK 3 S31: -0.1402 S32: -0.5763 S33: 0.1054 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 240:341) REMARK 3 ORIGIN FOR THE GROUP (A): 40.6375 16.3305 -3.0914 REMARK 3 T TENSOR REMARK 3 T11: 0.3662 T22: 0.3258 REMARK 3 T33: 0.2872 T12: 0.0981 REMARK 3 T13: 0.0390 T23: 0.0216 REMARK 3 L TENSOR REMARK 3 L11: 2.0097 L22: 0.7878 REMARK 3 L33: 1.2775 L12: -0.7209 REMARK 3 L13: -0.1956 L23: 0.2611 REMARK 3 S TENSOR REMARK 3 S11: 0.1114 S12: 0.0779 S13: 0.2153 REMARK 3 S21: -0.0494 S22: -0.1379 S23: -0.1116 REMARK 3 S31: 0.3881 S32: 0.1563 S33: 0.0116 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN P AND RESID 1:13) REMARK 3 ORIGIN FOR THE GROUP (A): 28.1001 30.2915 -0.0767 REMARK 3 T TENSOR REMARK 3 T11: 0.4609 T22: 0.3277 REMARK 3 T33: 0.5841 T12: -0.0521 REMARK 3 T13: -0.0872 T23: 0.0271 REMARK 3 L TENSOR REMARK 3 L11: 0.4435 L22: 0.2238 REMARK 3 L33: 0.5357 L12: -0.0716 REMARK 3 L13: -0.3482 L23: -0.0813 REMARK 3 S TENSOR REMARK 3 S11: 0.2334 S12: -0.0397 S13: 0.2848 REMARK 3 S21: -0.3250 S22: 0.2298 S23: 0.5278 REMARK 3 S31: 0.2602 S32: 0.1355 S33: -0.2807 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN T AND RESID 2:17) REMARK 3 ORIGIN FOR THE GROUP (A): 31.0726 27.2991 1.1114 REMARK 3 T TENSOR REMARK 3 T11: 0.3968 T22: 0.3697 REMARK 3 T33: 0.4273 T12: 0.0856 REMARK 3 T13: -0.0439 T23: 0.0098 REMARK 3 L TENSOR REMARK 3 L11: 0.8500 L22: 1.2942 REMARK 3 L33: 0.3052 L12: 0.6621 REMARK 3 L13: -0.7318 L23: 0.3573 REMARK 3 S TENSOR REMARK 3 S11: -0.0503 S12: -0.1985 S13: 0.3922 REMARK 3 S21: 0.0953 S22: 0.0360 S23: 0.3970 REMARK 3 S31: 0.1546 S32: 0.4484 S33: -0.0148 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 3PR4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000062718. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRADED MULTILAYER (OSMIC) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15419 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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) : 2.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1JX4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 3350, 0.15M CAAC2, 0.1M HEPES REMARK 280 PH 7.0, 2.5% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298.15K 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 48.17350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.00200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 48.17350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.00200 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: 5280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -75.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P, T REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 DT T 0 REMARK 465 DT T 1 REMARK 465 DC T 2 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 LYS A 24 CG CD CE NZ REMARK 470 LYS A 26 CG CD CE NZ REMARK 470 GLU A 38 CG CD OE1 OE2 REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 GLU A 94 CG CD OE1 OE2 REMARK 470 GLU A 97 CG CD OE1 OE2 REMARK 470 LYS A 98 CG CD CE NZ REMARK 470 LYS A 114 CG CD CE NZ REMARK 470 ARG A 116 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 169 CG CD OE1 OE2 REMARK 470 ARG A 176 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 200 CG OD1 ND2 REMARK 470 GLU A 209 CG CD OE1 OE2 REMARK 470 LYS A 212 CG CD CE NZ REMARK 470 GLU A 235 CG CD OE1 OE2 REMARK 470 ARG A 238 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 252 CG CD CE NZ REMARK 470 LYS A 278 CG CD CE NZ REMARK 470 GLU A 327 CG CD OE1 OE2 REMARK 470 DC P 13 O3' 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 DG T 7 O3' DG T 7 C3' -0.041 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG P 1 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG P 2 C3' - C2' - C1' ANGL. DEV. = -6.0 DEGREES REMARK 500 DG P 4 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA P 7 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC P 11 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT P 12 O5' - C5' - C4' ANGL. DEV. = -4.8 DEGREES REMARK 500 DC P 13 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DA T 3 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG T 5 C1' - O4' - C4' ANGL. DEV. = -6.6 DEGREES REMARK 500 DG T 7 O4' - C1' - N9 ANGL. DEV. = 6.6 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 56.56 21.18 REMARK 500 GLU A 38 109.47 -56.16 REMARK 500 ASP A 39 2.42 82.52 REMARK 500 SER A 96 142.97 -171.42 REMARK 500 ASP A 105 31.76 -140.51 REMARK 500 SER A 145 -164.42 -162.91 REMARK 500 ASN A 161 18.37 49.43 REMARK 500 LYS A 193 -39.50 -36.27 REMARK 500 ASP A 292 31.11 -99.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 ATP A 342 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 343 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD2 REMARK 620 2 PHE A 8 O 95.5 REMARK 620 3 ASP A 105 OD2 92.6 96.7 REMARK 620 4 ATP A 342 O1B 103.9 131.1 126.1 REMARK 620 5 ATP A 342 O2A 171.1 90.6 93.1 67.2 REMARK 620 6 HOH A 383 O 84.3 156.5 59.9 71.1 92.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 344 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD1 REMARK 620 2 GLU A 106 OE1 96.6 REMARK 620 3 HOH A 383 O 102.0 96.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 345 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 181 O REMARK 620 2 ILE A 186 O 88.6 REMARK 620 3 HOH A 381 O 73.7 62.6 REMARK 620 4 HOH A 398 O 76.9 164.5 107.4 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 ATP A 342 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 343 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 344 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 345 DBREF 3PR4 A 1 341 UNP Q97W02 DPO42_SULSO 1 341 DBREF 3PR4 T 0 17 PDB 3PR4 3PR4 0 17 DBREF 3PR4 P 1 13 PDB 3PR4 3PR4 1 13 SEQADV 3PR4 ALA A 12 UNP Q97W02 TYR 12 ENGINEERED MUTATION SEQRES 1 A 341 MET ILE VAL LEU PHE VAL ASP PHE ASP TYR PHE ALA 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 P 13 DG DG DG DG DG DA DA DG DG DA DC DT DC SEQRES 1 T 18 DT DT DC DA DT DG DA DG DT DC DC DT DT SEQRES 2 T 18 DC DC DC DC DC HET ATP A 342 26 HET CA A 343 1 HET CA A 344 1 HET CA A 345 1 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM CA CALCIUM ION FORMUL 4 ATP C10 H16 N5 O13 P3 FORMUL 5 CA 3(CA 2+) FORMUL 8 HOH *84(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 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 GLU A 325 1 19 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 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 SER A 338 -1 O PHE A 337 N ILE A 245 SHEET 3 C 4 ALA A 283 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 343 1555 1555 2.40 LINK OD1 ASP A 7 CA CA A 344 1555 1555 2.93 LINK O PHE A 8 CA CA A 343 1555 1555 2.36 LINK OD2 ASP A 105 CA CA A 343 1555 1555 2.36 LINK OE1 GLU A 106 CA CA A 344 1555 1555 2.82 LINK O ALA A 181 CA CA A 345 1555 1555 2.59 LINK O ILE A 186 CA CA A 345 1555 1555 2.52 LINK O1B ATP A 342 CA CA A 343 1555 1555 2.33 LINK O2A ATP A 342 CA CA A 343 1555 1555 2.42 LINK CA CA A 343 O HOH A 383 1555 1555 2.80 LINK CA CA A 344 O HOH A 383 1555 1555 2.92 LINK CA CA A 345 O HOH A 381 1555 1555 2.66 LINK CA CA A 345 O HOH A 398 1555 1555 2.87 CISPEP 1 LYS A 159 PRO A 160 0 3.22 SITE 1 AC1 19 PHE A 8 TYR A 10 PHE A 11 ALA A 12 SITE 2 AC1 19 ALA A 44 THR A 45 TYR A 48 ARG A 51 SITE 3 AC1 19 ASP A 105 LYS A 159 CA A 343 CA A 344 SITE 4 AC1 19 HOH A 359 HOH A 366 HOH A 383 HOH A 413 SITE 5 AC1 19 DC P 13 DT T 4 DG T 5 SITE 1 AC2 5 ASP A 7 PHE A 8 ASP A 105 ATP A 342 SITE 2 AC2 5 HOH A 383 SITE 1 AC3 6 ASP A 7 GLU A 106 LYS A 159 ATP A 342 SITE 2 AC3 6 HOH A 383 DC P 13 SITE 1 AC4 4 ALA A 181 ILE A 186 HOH A 381 HOH A 398 CRYST1 96.347 102.004 52.226 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 0.010379 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009804 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019148 0.00000