PDB Short entry for 3PR5 HEADER TRANSFERASE/DNA 29-NOV-10 3PR5 TITLE DPO4 Y12A MUTANT INCORPORATING ADP OPPOSITE TEMPLATE DT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE IV; COMPND 3 CHAIN: B; 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,H.LING REVDAT 3 06-SEP-23 3PR5 1 REMARK SEQADV LINK REVDAT 2 23-MAR-11 3PR5 1 JRNL REVDAT 1 23-FEB-11 3PR5 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. 2.40 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 19626 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.080 REMARK 3 FREE R VALUE TEST SET COUNT : 801 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 26.2946 - 4.3556 0.92 3198 133 0.2095 0.2188 REMARK 3 2 4.3556 - 3.4597 0.98 3271 133 0.1996 0.2537 REMARK 3 3 3.4597 - 3.0230 0.98 3208 139 0.2237 0.3012 REMARK 3 4 3.0230 - 2.7470 0.97 3130 140 0.2794 0.3103 REMARK 3 5 2.7470 - 2.5503 0.94 3054 129 0.2988 0.3418 REMARK 3 6 2.5503 - 2.4000 0.92 2964 127 0.3292 0.3412 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 51.53 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.130 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) : 10.82020 REMARK 3 B22 (A**2) : -4.74780 REMARK 3 B33 (A**2) : -6.07240 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 3441 REMARK 3 ANGLE : 1.316 4748 REMARK 3 CHIRALITY : 0.081 541 REMARK 3 PLANARITY : 0.004 501 REMARK 3 DIHEDRAL : 18.994 1376 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN B AND RESID 1:91) REMARK 3 ORIGIN FOR THE GROUP (A): -17.4259 5.3735 -6.1482 REMARK 3 T TENSOR REMARK 3 T11: 0.4048 T22: 0.4541 REMARK 3 T33: 0.3703 T12: 0.0925 REMARK 3 T13: 0.0132 T23: 0.0124 REMARK 3 L TENSOR REMARK 3 L11: 0.7911 L22: 1.5550 REMARK 3 L33: 1.1945 L12: 0.1076 REMARK 3 L13: 1.6394 L23: -0.0553 REMARK 3 S TENSOR REMARK 3 S11: -0.0502 S12: -0.0492 S13: -0.1316 REMARK 3 S21: 0.1181 S22: 0.1524 S23: 0.1008 REMARK 3 S31: 0.1261 S32: 0.2183 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN B AND RESID 92:222) REMARK 3 ORIGIN FOR THE GROUP (A): -35.2030 19.9130 -8.5199 REMARK 3 T TENSOR REMARK 3 T11: 0.2477 T22: 0.3691 REMARK 3 T33: 0.3508 T12: 0.0491 REMARK 3 T13: -0.0126 T23: -0.0457 REMARK 3 L TENSOR REMARK 3 L11: 1.5174 L22: 2.5120 REMARK 3 L33: 1.4527 L12: -0.3046 REMARK 3 L13: -0.2834 L23: -0.0596 REMARK 3 S TENSOR REMARK 3 S11: -0.2395 S12: -0.3388 S13: 0.0321 REMARK 3 S21: 0.1876 S22: 0.2104 S23: 0.4062 REMARK 3 S31: -0.0510 S32: -0.0817 S33: -0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN B AND RESID 223:239) REMARK 3 ORIGIN FOR THE GROUP (A): -37.3273 27.8098 -16.0878 REMARK 3 T TENSOR REMARK 3 T11: 0.5545 T22: 0.4973 REMARK 3 T33: 0.4818 T12: 0.0333 REMARK 3 T13: -0.1981 T23: -0.0695 REMARK 3 L TENSOR REMARK 3 L11: 0.3670 L22: 0.1970 REMARK 3 L33: 0.1096 L12: 0.6210 REMARK 3 L13: -0.2334 L23: -0.4263 REMARK 3 S TENSOR REMARK 3 S11: -0.0148 S12: -0.0096 S13: -0.0248 REMARK 3 S21: -1.1576 S22: -0.1154 S23: 0.6074 REMARK 3 S31: -0.3477 S32: -0.6652 S33: -0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 240:341) REMARK 3 ORIGIN FOR THE GROUP (A): -7.4864 16.3002 -29.1926 REMARK 3 T TENSOR REMARK 3 T11: 0.4650 T22: 0.4510 REMARK 3 T33: 0.3922 T12: 0.0737 REMARK 3 T13: 0.0872 T23: -0.0086 REMARK 3 L TENSOR REMARK 3 L11: 2.2666 L22: 1.6467 REMARK 3 L33: 3.3031 L12: -0.9189 REMARK 3 L13: -0.3207 L23: 0.4313 REMARK 3 S TENSOR REMARK 3 S11: -0.0066 S12: -0.0237 S13: 0.2323 REMARK 3 S21: -0.0002 S22: -0.1313 S23: -0.0590 REMARK 3 S31: 0.2720 S32: 0.2996 S33: 0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN P AND RESID 1:13) REMARK 3 ORIGIN FOR THE GROUP (A): -20.0450 30.3522 -26.2127 REMARK 3 T TENSOR REMARK 3 T11: 0.5145 T22: 0.2462 REMARK 3 T33: 0.3809 T12: -0.0776 REMARK 3 T13: -0.0761 T23: 0.0111 REMARK 3 L TENSOR REMARK 3 L11: 1.0050 L22: 0.0201 REMARK 3 L33: 0.3255 L12: -0.0327 REMARK 3 L13: -0.4074 L23: 0.6148 REMARK 3 S TENSOR REMARK 3 S11: 0.1400 S12: -0.5204 S13: 0.0916 REMARK 3 S21: -0.1735 S22: -0.0497 S23: 0.3427 REMARK 3 S31: 0.6058 S32: 0.0032 S33: -0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN T AND RESID 3:17) REMARK 3 ORIGIN FOR THE GROUP (A): -17.1001 27.3813 -25.0517 REMARK 3 T TENSOR REMARK 3 T11: 0.5081 T22: 0.3170 REMARK 3 T33: 0.3316 T12: 0.0296 REMARK 3 T13: -0.0364 T23: 0.0334 REMARK 3 L TENSOR REMARK 3 L11: 0.5179 L22: 1.2272 REMARK 3 L33: -0.0525 L12: 1.0814 REMARK 3 L13: -1.3786 L23: 0.8173 REMARK 3 S TENSOR REMARK 3 S11: -0.1195 S12: -0.3337 S13: 0.0794 REMARK 3 S21: 0.3710 S22: -0.4329 S23: -0.4465 REMARK 3 S31: 0.2081 S32: 0.4742 S33: -0.0000 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 3PR5 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_1000062719. 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19626 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 95.1 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) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.9 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 (%): 53.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 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 47.80350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.99650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.80350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.99650 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: 19900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 DT T 4 P DT T 4 O5' 0.091 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 2 C3' - C2' - C1' ANGL. DEV. = -6.4 DEGREES REMARK 500 DG P 2 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA P 10 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC P 13 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT T 4 O5' - P - OP1 ANGL. DEV. = -9.4 DEGREES REMARK 500 DT T 4 C2 - N3 - C4 ANGL. DEV. = -4.0 DEGREES REMARK 500 DG T 5 N1 - C2 - N2 ANGL. DEV. = 6.8 DEGREES REMARK 500 DG T 5 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES REMARK 500 DG T 5 N1 - C6 - O6 ANGL. DEV. = 6.3 DEGREES REMARK 500 DG T 5 C5 - C6 - O6 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG T 7 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 DC T 10 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC T 14 O4' - C1' - N1 ANGL. DEV. = 1.9 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 B 10 56.19 25.54 REMARK 500 ASP B 113 33.70 -89.57 REMARK 500 LYS B 114 -34.63 -136.57 REMARK 500 SER B 145 -169.99 -175.79 REMARK 500 ASP B 277 85.89 30.88 REMARK 500 LYS B 278 -27.76 86.15 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 B 344 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 B 343 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 7 OD1 REMARK 620 2 PHE B 8 O 86.7 REMARK 620 3 ASP B 105 OD2 100.7 84.6 REMARK 620 4 ATP B 344 O1A 177.6 92.4 77.0 REMARK 620 5 ATP B 344 O1B 89.8 138.0 137.0 92.4 REMARK 620 6 HOH B 398 O 77.3 152.0 76.2 102.7 65.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 342 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 181 O REMARK 620 2 ILE B 186 O 81.4 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 342 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 343 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP B 344 DBREF 3PR5 B 1 341 UNP Q97W02 DPO42_SULSO 1 341 DBREF 3PR5 T 0 17 PDB 3PR5 3PR5 0 17 DBREF 3PR5 P 1 13 PDB 3PR5 3PR5 1 13 SEQADV 3PR5 ALA B 12 UNP Q97W02 TYR 12 ENGINEERED MUTATION SEQRES 1 B 341 MET ILE VAL LEU PHE VAL ASP PHE ASP TYR PHE ALA ALA SEQRES 2 B 341 GLN VAL GLU GLU VAL LEU ASN PRO SER LEU LYS GLY LYS SEQRES 3 B 341 PRO VAL VAL VAL CYS VAL PHE SER GLY ARG PHE GLU ASP SEQRES 4 B 341 SER GLY ALA VAL ALA THR ALA ASN TYR GLU ALA ARG LYS SEQRES 5 B 341 PHE GLY VAL LYS ALA GLY ILE PRO ILE VAL GLU ALA LYS SEQRES 6 B 341 LYS ILE LEU PRO ASN ALA VAL TYR LEU PRO MET ARG LYS SEQRES 7 B 341 GLU VAL TYR GLN GLN VAL SER SER ARG ILE MET ASN LEU SEQRES 8 B 341 LEU ARG GLU TYR SER GLU LYS ILE GLU ILE ALA SER ILE SEQRES 9 B 341 ASP GLU ALA TYR LEU ASP ILE SER ASP LYS VAL ARG ASP SEQRES 10 B 341 TYR ARG GLU ALA TYR ASN LEU GLY LEU GLU ILE LYS ASN SEQRES 11 B 341 LYS ILE LEU GLU LYS GLU LYS ILE THR VAL THR VAL GLY SEQRES 12 B 341 ILE SER LYS ASN LYS VAL PHE ALA LYS ILE ALA ALA ASP SEQRES 13 B 341 MET ALA LYS PRO ASN GLY ILE LYS VAL ILE ASP ASP GLU SEQRES 14 B 341 GLU VAL LYS ARG LEU ILE ARG GLU LEU ASP ILE ALA ASP SEQRES 15 B 341 VAL PRO GLY ILE GLY ASN ILE THR ALA GLU LYS LEU LYS SEQRES 16 B 341 LYS LEU GLY ILE ASN LYS LEU VAL ASP THR LEU SER ILE SEQRES 17 B 341 GLU PHE ASP LYS LEU LYS GLY MET ILE GLY GLU ALA LYS SEQRES 18 B 341 ALA LYS TYR LEU ILE SER LEU ALA ARG ASP GLU TYR ASN SEQRES 19 B 341 GLU PRO ILE ARG THR ARG VAL ARG LYS SER ILE GLY ARG SEQRES 20 B 341 ILE VAL THR MET LYS ARG ASN SER ARG ASN LEU GLU GLU SEQRES 21 B 341 ILE LYS PRO TYR LEU PHE ARG ALA ILE GLU GLU SER TYR SEQRES 22 B 341 TYR LYS LEU ASP LYS ARG ILE PRO LYS ALA ILE HIS VAL SEQRES 23 B 341 VAL ALA VAL THR GLU ASP LEU ASP ILE VAL SER ARG GLY SEQRES 24 B 341 ARG THR PHE PRO HIS GLY ILE SER LYS GLU THR ALA TYR SEQRES 25 B 341 SER GLU SER VAL LYS LEU LEU GLN LYS ILE LEU GLU GLU SEQRES 26 B 341 ASP GLU ARG LYS ILE ARG ARG ILE GLY VAL ARG PHE SER SEQRES 27 B 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 CA B 342 1 HET CA B 343 1 HET ATP B 344 27 HETNAM CA CALCIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 4 CA 2(CA 2+) FORMUL 6 ATP C10 H16 N5 O13 P3 FORMUL 7 HOH *77(H2 O) HELIX 1 1 TYR B 10 ASN B 20 1 11 HELIX 2 2 PRO B 21 LYS B 24 5 4 HELIX 3 3 ASN B 47 LYS B 52 1 6 HELIX 4 4 PRO B 60 LEU B 68 1 9 HELIX 5 5 ARG B 77 ARG B 93 1 17 HELIX 6 6 ASP B 117 LYS B 137 1 21 HELIX 7 7 ASN B 147 LYS B 159 1 13 HELIX 8 8 ASP B 167 LEU B 178 1 12 HELIX 9 9 ASP B 179 VAL B 183 5 5 HELIX 10 10 GLY B 187 LYS B 196 1 10 HELIX 11 11 LEU B 202 SER B 207 5 6 HELIX 12 12 GLU B 209 GLY B 218 1 10 HELIX 13 13 GLY B 218 ARG B 230 1 13 HELIX 14 14 ASN B 257 ASP B 277 1 21 HELIX 15 15 SER B 307 GLU B 325 1 19 SHEET 1 A 5 ILE B 99 SER B 103 0 SHEET 2 A 5 GLU B 106 ASP B 110 -1 O TYR B 108 N GLU B 100 SHEET 3 A 5 VAL B 3 PHE B 8 -1 N VAL B 6 O ALA B 107 SHEET 4 A 5 VAL B 140 SER B 145 -1 O GLY B 143 N PHE B 5 SHEET 5 A 5 ILE B 163 VAL B 165 1 O LYS B 164 N ILE B 144 SHEET 1 B 3 GLY B 41 ALA B 46 0 SHEET 2 B 3 VAL B 28 PHE B 33 -1 N VAL B 30 O ALA B 44 SHEET 3 B 3 VAL B 72 PRO B 75 1 O LEU B 74 N CYS B 31 SHEET 1 C 4 SER B 244 SER B 255 0 SHEET 2 C 4 ILE B 330 PHE B 340 -1 O ILE B 330 N SER B 255 SHEET 3 C 4 PRO B 281 THR B 290 -1 N VAL B 289 O ARG B 331 SHEET 4 C 4 ILE B 295 THR B 301 -1 O ARG B 298 N VAL B 286 LINK OD1 ASP B 7 CA CA B 343 1555 1555 2.40 LINK O PHE B 8 CA CA B 343 1555 1555 2.39 LINK OD2 ASP B 105 CA CA B 343 1555 1555 2.61 LINK O ALA B 181 CA CA B 342 1555 1555 2.53 LINK O ILE B 186 CA CA B 342 1555 1555 2.69 LINK CA CA B 343 O1A ATP B 344 1555 1555 2.45 LINK CA CA B 343 O1B ATP B 344 1555 1555 2.75 LINK CA CA B 343 O HOH B 398 1555 1555 2.84 CISPEP 1 LYS B 159 PRO B 160 0 4.59 SITE 1 AC1 2 ALA B 181 ILE B 186 SITE 1 AC2 5 ASP B 7 PHE B 8 ASP B 105 ATP B 344 SITE 2 AC2 5 HOH B 398 SITE 1 AC3 18 ASP B 7 PHE B 8 TYR B 10 PHE B 11 SITE 2 AC3 18 ALA B 12 ALA B 44 THR B 45 TYR B 48 SITE 3 AC3 18 ARG B 51 ALA B 57 ASP B 105 LYS B 159 SITE 4 AC3 18 CA B 343 HOH B 346 HOH B 398 DC P 13 SITE 5 AC3 18 DT T 4 DG T 5 CRYST1 95.607 101.993 52.288 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 0.010459 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009805 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019125 0.00000