HEADER HYDROLASE 16-DEC-22 8HRV TITLE DUTPASE OF HELICOBACTER PYLORI 26695 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: DUTPASE,DUTP PYROPHOSPHATASE; COMPND 5 EC: 3.6.1.23; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI 26695; SOURCE 3 ORGANISM_COMMON: CAMPYLOBACTER PYLORI; SOURCE 4 ORGANISM_TAXID: 85962; SOURCE 5 STRAIN: 26695; SOURCE 6 GENE: DUT, HP_0865; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.KUMARI,S.GOURINATH REVDAT 1 17-JAN-24 8HRV 0 JRNL AUTH K.KUMARI,S.GOURINATH JRNL TITL DUTPASE OF HELICOBACTER PYLORI 26695 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0352 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 32675 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.001 REMARK 3 FREE R VALUE TEST SET COUNT : 1634 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2269 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.1860 REMARK 3 BIN FREE R VALUE SET COUNT : 108 REMARK 3 BIN FREE R VALUE : 0.2050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3264 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 91 REMARK 3 SOLVENT ATOMS : 246 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.46700 REMARK 3 B22 (A**2) : 0.46700 REMARK 3 B33 (A**2) : -1.51500 REMARK 3 B12 (A**2) : 0.23300 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): 0.138 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.126 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.492 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3429 ; 0.009 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3152 ; 0.002 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4658 ; 1.442 ; 1.638 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7352 ; 0.483 ; 1.552 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 442 ; 6.577 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 15 ; 8.149 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 569 ;13.271 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 548 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3841 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 611 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 496 ; 0.221 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 19 ; 0.157 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1640 ; 0.163 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 230 ; 0.135 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.039 ; 0.200 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): 1745 ; 1.989 ; 2.007 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1745 ; 1.985 ; 2.006 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2179 ; 2.824 ; 2.991 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2180 ; 2.824 ; 2.993 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1684 ; 3.256 ; 2.315 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1678 ; 3.259 ; 2.315 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2473 ; 4.978 ; 3.321 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2474 ; 4.977 ; 3.321 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 : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 0 A 142 NULL REMARK 3 1 A 0 A 142 NULL REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 2 A 0 A 142 NULL REMARK 3 2 A 0 A 142 NULL REMARK 3 GROUP CHAIN COUNT RMS WEIGHT 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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 286 REMARK 3 ORIGIN FOR THE GROUP (A): -23.5406 25.6330 7.0394 REMARK 3 T TENSOR REMARK 3 T11: 0.0450 T22: 0.0265 REMARK 3 T33: 0.0179 T12: -0.0131 REMARK 3 T13: -0.0102 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 0.0760 L22: 0.6556 REMARK 3 L33: 0.3984 L12: 0.0862 REMARK 3 L13: 0.1327 L23: 0.3251 REMARK 3 S TENSOR REMARK 3 S11: 0.0308 S12: 0.0127 S13: 0.0082 REMARK 3 S21: 0.0384 S22: -0.0548 S23: -0.0069 REMARK 3 S31: -0.0056 S32: 0.0383 S33: 0.0240 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): -28.9739 20.3162 -5.7122 REMARK 3 T TENSOR REMARK 3 T11: 0.0408 T22: 0.0298 REMARK 3 T33: 0.0154 T12: 0.0104 REMARK 3 T13: -0.0171 T23: -0.0117 REMARK 3 L TENSOR REMARK 3 L11: 0.2287 L22: 1.2717 REMARK 3 L33: 0.1532 L12: 0.2468 REMARK 3 L13: 0.1732 L23: 0.2508 REMARK 3 S TENSOR REMARK 3 S11: 0.0413 S12: 0.0539 S13: -0.0135 REMARK 3 S21: -0.0502 S22: -0.0446 S23: 0.0715 REMARK 3 S31: 0.0075 S32: 0.0429 S33: 0.0033 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): -20.4496 32.0531 -5.8651 REMARK 3 T TENSOR REMARK 3 T11: 0.0516 T22: 0.0156 REMARK 3 T33: 0.0105 T12: -0.0147 REMARK 3 T13: 0.0190 T23: -0.0017 REMARK 3 L TENSOR REMARK 3 L11: 0.3719 L22: 0.9323 REMARK 3 L33: 0.2376 L12: 0.4165 REMARK 3 L13: -0.2005 L23: -0.0035 REMARK 3 S TENSOR REMARK 3 S11: -0.0401 S12: 0.0470 S13: -0.0226 REMARK 3 S21: -0.1381 S22: 0.0490 S23: -0.0831 REMARK 3 S31: -0.0155 S32: -0.0181 S33: -0.0089 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8HRV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1300034195. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9805 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32696 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 89.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.30 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 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: NULL REMARK 200 REMARK 200 REMARK: ROD SHAPED CRYSTALS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M AMINO ACID MIX,0.1 M BUFFER REMARK 280 SYSTEM1 PH 6.5, 50% V/V PRECIPITANT MIX4, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.32550 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 39.32550 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.32550 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: 16700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -87.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 LYS A 144 REMARK 465 ALA A 145 REMARK 465 HIS A 146 REMARK 465 HIS A 147 REMARK 465 HIS A 148 REMARK 465 HIS A 149 REMARK 465 HIS A 150 REMARK 465 HIS A 151 REMARK 465 ALA B 145 REMARK 465 HIS B 146 REMARK 465 HIS B 147 REMARK 465 HIS B 148 REMARK 465 HIS B 149 REMARK 465 HIS B 150 REMARK 465 HIS B 151 REMARK 465 ALA C 145 REMARK 465 HIS C 146 REMARK 465 HIS C 147 REMARK 465 HIS C 148 REMARK 465 HIS C 149 REMARK 465 HIS C 150 REMARK 465 HIS C 151 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 36 CE NZ REMARK 470 LYS A 98 CE NZ REMARK 470 GLU A 125 OE1 OE2 REMARK 470 GLN A 126 CD OE1 NE2 REMARK 470 LYS B 2 NZ REMARK 470 LYS B 4 NZ REMARK 470 LYS B 16 NZ REMARK 470 LYS B 36 CE NZ REMARK 470 LYS B 98 CE NZ REMARK 470 LYS B 118 CG CD CE NZ REMARK 470 GLU B 120 CG CD OE1 OE2 REMARK 470 GLU B 129 CD OE1 OE2 REMARK 470 LYS B 144 CG CD CE NZ REMARK 470 LYS C 2 CE NZ REMARK 470 LYS C 16 CG CD CE NZ REMARK 470 LYS C 36 CG CD CE NZ REMARK 470 LYS C 98 CE NZ REMARK 470 LYS C 101 CG CD CE NZ REMARK 470 LYS C 144 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG B 85 0.08 SIDE CHAIN 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 MG C 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DUP A 301 O1A REMARK 620 2 DUP A 301 O2B 88.4 REMARK 620 3 DUP A 301 O3G 94.7 92.7 REMARK 620 4 HOH A 457 O 86.9 175.3 87.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DUP B 203 O2A REMARK 620 2 DUP B 203 O2B 83.3 REMARK 620 3 DUP B 203 O1G 95.1 87.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DUP C 201 O1B REMARK 620 2 DUP C 201 O2A 89.7 REMARK 620 3 DUP C 201 O2G 85.1 95.8 REMARK 620 N 1 2 DBREF 8HRV A 1 145 UNP O25536 DUT_HELPY 1 145 DBREF 8HRV B 1 145 UNP O25536 DUT_HELPY 1 145 DBREF 8HRV C 1 145 UNP O25536 DUT_HELPY 1 145 SEQADV 8HRV ALA A 0 UNP O25536 EXPRESSION TAG SEQADV 8HRV HIS A 146 UNP O25536 EXPRESSION TAG SEQADV 8HRV HIS A 147 UNP O25536 EXPRESSION TAG SEQADV 8HRV HIS A 148 UNP O25536 EXPRESSION TAG SEQADV 8HRV HIS A 149 UNP O25536 EXPRESSION TAG SEQADV 8HRV HIS A 150 UNP O25536 EXPRESSION TAG SEQADV 8HRV HIS A 151 UNP O25536 EXPRESSION TAG SEQADV 8HRV ALA B 0 UNP O25536 EXPRESSION TAG SEQADV 8HRV HIS B 146 UNP O25536 EXPRESSION TAG SEQADV 8HRV HIS B 147 UNP O25536 EXPRESSION TAG SEQADV 8HRV HIS B 148 UNP O25536 EXPRESSION TAG SEQADV 8HRV HIS B 149 UNP O25536 EXPRESSION TAG SEQADV 8HRV HIS B 150 UNP O25536 EXPRESSION TAG SEQADV 8HRV HIS B 151 UNP O25536 EXPRESSION TAG SEQADV 8HRV ALA C 0 UNP O25536 EXPRESSION TAG SEQADV 8HRV HIS C 146 UNP O25536 EXPRESSION TAG SEQADV 8HRV HIS C 147 UNP O25536 EXPRESSION TAG SEQADV 8HRV HIS C 148 UNP O25536 EXPRESSION TAG SEQADV 8HRV HIS C 149 UNP O25536 EXPRESSION TAG SEQADV 8HRV HIS C 150 UNP O25536 EXPRESSION TAG SEQADV 8HRV HIS C 151 UNP O25536 EXPRESSION TAG SEQRES 1 A 152 ALA MET LYS ILE LYS ILE GLN LYS ILE HIS PRO ASN ALA SEQRES 2 A 152 LEU ILE PRO LYS TYR GLN THR ASP GLY SER SER GLY PHE SEQRES 3 A 152 ASP LEU HIS ALA VAL GLU GLU VAL MET ILE LYS PRO HIS SEQRES 4 A 152 SER VAL GLY LEU VAL LYS ILE GLY ILE CYS LEU SER LEU SEQRES 5 A 152 GLU VAL GLY TYR GLU LEU GLN VAL ARG THR ARG SER GLY SEQRES 6 A 152 LEU ALA LEU ASN HIS GLN VAL MET VAL LEU ASN SER PRO SEQRES 7 A 152 GLY THR VAL ASP ASN ASP TYR ARG GLY GLU ILE LYS VAL SEQRES 8 A 152 ILE LEU ALA ASN LEU SER ASP LYS ASP PHE LYS VAL GLN SEQRES 9 A 152 VAL GLY ASP ARG ILE ALA GLN GLY VAL VAL GLN LYS THR SEQRES 10 A 152 TYR LYS ALA GLU PHE ILE GLU CYS GLU GLN LEU ASP GLU SEQRES 11 A 152 THR SER ARG GLY SER GLY GLY PHE GLY SER THR GLY VAL SEQRES 12 A 152 SER LYS ALA HIS HIS HIS HIS HIS HIS SEQRES 1 B 152 ALA MET LYS ILE LYS ILE GLN LYS ILE HIS PRO ASN ALA SEQRES 2 B 152 LEU ILE PRO LYS TYR GLN THR ASP GLY SER SER GLY PHE SEQRES 3 B 152 ASP LEU HIS ALA VAL GLU GLU VAL MET ILE LYS PRO HIS SEQRES 4 B 152 SER VAL GLY LEU VAL LYS ILE GLY ILE CYS LEU SER LEU SEQRES 5 B 152 GLU VAL GLY TYR GLU LEU GLN VAL ARG THR ARG SER GLY SEQRES 6 B 152 LEU ALA LEU ASN HIS GLN VAL MET VAL LEU ASN SER PRO SEQRES 7 B 152 GLY THR VAL ASP ASN ASP TYR ARG GLY GLU ILE LYS VAL SEQRES 8 B 152 ILE LEU ALA ASN LEU SER ASP LYS ASP PHE LYS VAL GLN SEQRES 9 B 152 VAL GLY ASP ARG ILE ALA GLN GLY VAL VAL GLN LYS THR SEQRES 10 B 152 TYR LYS ALA GLU PHE ILE GLU CYS GLU GLN LEU ASP GLU SEQRES 11 B 152 THR SER ARG GLY SER GLY GLY PHE GLY SER THR GLY VAL SEQRES 12 B 152 SER LYS ALA HIS HIS HIS HIS HIS HIS SEQRES 1 C 152 ALA MET LYS ILE LYS ILE GLN LYS ILE HIS PRO ASN ALA SEQRES 2 C 152 LEU ILE PRO LYS TYR GLN THR ASP GLY SER SER GLY PHE SEQRES 3 C 152 ASP LEU HIS ALA VAL GLU GLU VAL MET ILE LYS PRO HIS SEQRES 4 C 152 SER VAL GLY LEU VAL LYS ILE GLY ILE CYS LEU SER LEU SEQRES 5 C 152 GLU VAL GLY TYR GLU LEU GLN VAL ARG THR ARG SER GLY SEQRES 6 C 152 LEU ALA LEU ASN HIS GLN VAL MET VAL LEU ASN SER PRO SEQRES 7 C 152 GLY THR VAL ASP ASN ASP TYR ARG GLY GLU ILE LYS VAL SEQRES 8 C 152 ILE LEU ALA ASN LEU SER ASP LYS ASP PHE LYS VAL GLN SEQRES 9 C 152 VAL GLY ASP ARG ILE ALA GLN GLY VAL VAL GLN LYS THR SEQRES 10 C 152 TYR LYS ALA GLU PHE ILE GLU CYS GLU GLN LEU ASP GLU SEQRES 11 C 152 THR SER ARG GLY SER GLY GLY PHE GLY SER THR GLY VAL SEQRES 12 C 152 SER LYS ALA HIS HIS HIS HIS HIS HIS HET DUP A 301 28 HET MG A 302 1 HET MG B 201 1 HET EDO B 202 4 HET DUP B 203 28 HET DUP C 201 28 HET MG C 202 1 HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 4 DUP 3(C9 H16 N3 O13 P3) FORMUL 5 MG 3(MG 2+) FORMUL 7 EDO C2 H6 O2 FORMUL 11 HOH *246(H2 O) HELIX 1 AA1 ARG A 62 GLN A 70 1 9 HELIX 2 AA2 ARG B 62 GLN B 70 1 9 HELIX 3 AA3 ARG C 62 GLN C 70 1 9 SHEET 1 AA1 5 VAL A 71 VAL A 73 0 SHEET 2 AA1 5 GLU A 87 ASN A 94 -1 O ALA A 93 N MET A 72 SHEET 3 AA1 5 SER A 39 LEU A 51 -1 N VAL A 43 O VAL A 90 SHEET 4 AA1 5 MET A 1 LYS A 7 -1 N GLN A 6 O CYS A 48 SHEET 5 AA1 5 ALA C 119 GLU C 123 1 O ILE C 122 N ILE A 3 SHEET 1 AA2 5 LYS A 16 TYR A 17 0 SHEET 2 AA2 5 PHE A 25 HIS A 28 -1 O ASP A 26 N LYS A 16 SHEET 3 AA2 5 ARG A 107 LYS A 115 -1 O GLY A 111 N PHE A 25 SHEET 4 AA2 5 TYR A 55 ARG A 60 -1 N ARG A 60 O GLN A 110 SHEET 5 AA2 5 GLY A 78 VAL A 80 -1 O GLY A 78 N VAL A 59 SHEET 1 AA3 2 VAL A 33 ILE A 35 0 SHEET 2 AA3 2 PHE A 100 VAL A 102 -1 O VAL A 102 N VAL A 33 SHEET 1 AA4 5 ALA A 119 GLU A 123 0 SHEET 2 AA4 5 MET B 1 LYS B 7 1 O ILE B 3 N ILE A 122 SHEET 3 AA4 5 SER B 39 LEU B 51 -1 O CYS B 48 N GLN B 6 SHEET 4 AA4 5 GLU B 87 ASN B 94 -1 O VAL B 90 N VAL B 43 SHEET 5 AA4 5 VAL B 71 VAL B 73 -1 N MET B 72 O ALA B 93 SHEET 1 AA5 4 PHE B 25 HIS B 28 0 SHEET 2 AA5 4 ARG B 107 LYS B 115 -1 O GLY B 111 N PHE B 25 SHEET 3 AA5 4 TYR B 55 ARG B 60 -1 N ARG B 60 O GLN B 110 SHEET 4 AA5 4 GLY B 78 VAL B 80 -1 O GLY B 78 N VAL B 59 SHEET 1 AA6 2 VAL B 33 ILE B 35 0 SHEET 2 AA6 2 PHE B 100 VAL B 102 -1 O PHE B 100 N ILE B 35 SHEET 1 AA7 5 ALA B 119 GLU B 123 0 SHEET 2 AA7 5 MET C 1 LYS C 7 1 O ILE C 3 N ILE B 122 SHEET 3 AA7 5 SER C 39 LEU C 51 -1 O CYS C 48 N GLN C 6 SHEET 4 AA7 5 GLU C 87 ASN C 94 -1 O VAL C 90 N VAL C 43 SHEET 5 AA7 5 VAL C 71 VAL C 73 -1 N MET C 72 O ALA C 93 SHEET 1 AA8 4 PHE C 25 HIS C 28 0 SHEET 2 AA8 4 ARG C 107 LYS C 115 -1 O GLY C 111 N PHE C 25 SHEET 3 AA8 4 TYR C 55 ARG C 60 -1 N ARG C 60 O GLN C 110 SHEET 4 AA8 4 GLY C 78 VAL C 80 -1 O GLY C 78 N VAL C 59 SHEET 1 AA9 2 VAL C 33 ILE C 35 0 SHEET 2 AA9 2 PHE C 100 VAL C 102 -1 O PHE C 100 N ILE C 35 LINK O1A DUP A 301 MG MG C 202 1555 1555 2.08 LINK O2B DUP A 301 MG MG C 202 1555 1555 1.94 LINK O3G DUP A 301 MG MG C 202 1555 1555 2.09 LINK MG MG A 302 O2A DUP B 203 1555 1555 2.07 LINK MG MG A 302 O2B DUP B 203 1555 1555 2.07 LINK MG MG A 302 O1G DUP B 203 1555 1555 2.07 LINK O HOH A 457 MG MG C 202 1555 1555 2.18 LINK MG MG B 201 O1B DUP C 201 1555 1555 2.04 LINK MG MG B 201 O2A DUP C 201 1555 1555 2.15 LINK MG MG B 201 O2G DUP C 201 1555 1555 2.15 CISPEP 1 SER A 76 PRO A 77 0 -6.23 CISPEP 2 SER B 76 PRO B 77 0 -8.65 CISPEP 3 SER C 76 PRO C 77 0 -7.15 CRYST1 103.869 103.869 78.651 90.00 90.00 120.00 P 63 18 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 0.009628 0.005558 0.000000 0.00000 SCALE2 0.000000 0.011117 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012714 0.00000