HEADER HYDROLASE 30-MAR-12 4AOZ TITLE B. SUBTILIS DUTPASE YNCF IN COMPLEX WITH DU, PPI AND MG (P212121) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE COMPND 3 YNCF; COMPND 4 CHAIN: A, B, C; COMPND 5 SYNONYM: DUTPASE, DUTP PYROPHOSPHATASE; COMPND 6 EC: 3.6.1.23; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.TIMM,J.GARCIA-NAFRIA,C.HARRISON,J.P.TURKENBURG,K.S.WILSON REVDAT 4 20-DEC-23 4AOZ 1 REMARK LINK REVDAT 3 07-AUG-13 4AOZ 1 JRNL REVDAT 2 31-JUL-13 4AOZ 1 AUTHOR JRNL REVDAT 1 01-MAY-13 4AOZ 0 JRNL AUTH J.GARCIA-NAFRIA,J.TIMM,C.HARRISON,J.P.TURKENBURG,K.S.WILSON JRNL TITL TYING DOWN THE ARM IN BACILLUS DUTPASE: STRUCTURE AND JRNL TITL 2 MECHANISM JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 69 1367 2013 JRNL REFN ISSN 0907-4449 JRNL PMID 23897460 JRNL DOI 10.1107/S090744491300735X REMARK 2 REMARK 2 RESOLUTION. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 28124 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1501 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1952 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.12 REMARK 3 BIN R VALUE (WORKING SET) : 0.1710 REMARK 3 BIN FREE R VALUE SET COUNT : 113 REMARK 3 BIN FREE R VALUE : 0.2360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3304 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 77 REMARK 3 SOLVENT ATOMS : 566 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.98000 REMARK 3 B22 (A**2) : 0.49000 REMARK 3 B33 (A**2) : 0.49000 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): 0.195 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.169 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.102 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.731 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3574 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2498 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4837 ; 1.612 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6119 ; 0.861 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 445 ; 6.562 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 167 ;32.719 ;24.731 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 677 ;14.160 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;17.836 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 523 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3907 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 704 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2119 ; 0.741 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 861 ; 0.177 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3443 ; 1.347 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1455 ; 2.282 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1378 ; 3.675 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4AOZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1290051927. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9173 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29682 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 50.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.400 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 2XCD REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NACL, 0.1M NA ACETATE PH 5, 20% REMARK 280 PEG 6K, PH 5.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 35.13500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.14950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.76700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.14950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.13500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.76700 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: 14700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -84.3 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 MET A 1 REMARK 465 ASN A 132 REMARK 465 GLU A 133 REMARK 465 ASP A 134 REMARK 465 ARG A 135 REMARK 465 GLY A 136 REMARK 465 GLY A 137 REMARK 465 LEU A 138 REMARK 465 GLY A 139 REMARK 465 SER A 140 REMARK 465 THR A 141 REMARK 465 GLY A 142 REMARK 465 THR A 143 REMARK 465 LYS A 144 REMARK 465 MET B 1 REMARK 465 MET C 1 REMARK 465 SER C 18 REMARK 465 LYS C 19 REMARK 465 ILE C 20 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 68 CE NZ REMARK 470 THR B 2 OG1 CG2 REMARK 470 GLU B 21 CG CD OE1 OE2 REMARK 470 GLN C 22 CG CD OE1 NE2 REMARK 470 LYS C 37 NZ 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 OE2 GLU C 128 O HOH C 2155 2.15 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 SER A 77 -70.87 68.58 REMARK 500 SER B 77 -69.12 72.87 REMARK 500 SER C 77 -76.30 69.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH C2038 DISTANCE = 6.46 ANGSTROMS REMARK 525 HOH C2060 DISTANCE = 7.03 ANGSTROMS REMARK 525 HOH C2135 DISTANCE = 9.87 ANGSTROMS 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 B1147 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2075 O REMARK 620 2 HOH A2076 O 84.9 REMARK 620 3 HOH A2183 O 166.9 85.7 REMARK 620 4 POP B1146 O2 95.3 176.3 94.6 REMARK 620 5 POP B1146 O5 90.5 86.8 98.1 89.5 REMARK 620 6 HOH B2172 O 92.2 83.8 77.7 99.9 170.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C1150 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2156 O REMARK 620 2 HOH B2052 O 95.8 REMARK 620 3 HOH B2053 O 166.2 80.8 REMARK 620 4 POP C1149 O2 87.5 174.2 97.1 REMARK 620 5 POP C1149 O5 99.5 88.5 93.8 86.2 REMARK 620 6 HOH C2160 O 76.1 86.9 90.3 98.6 173.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 1145 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 1146 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL C 1147 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUR A 1132 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUR B 1145 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUR C 1148 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP C 1149 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP B 1146 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 1150 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1147 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XCD RELATED DB: PDB REMARK 900 STRUCTURE OF YNCF,THE GENOMIC DUTPASE FROM BACILLUS SUBTILIS REMARK 900 RELATED ID: 2XCE RELATED DB: PDB REMARK 900 STRUCTURE OF YNCF IN COMPLEX WITH DUPNHPP REMARK 900 RELATED ID: 4AOO RELATED DB: PDB REMARK 900 B. SUBTILIS DUTPASE YNCF IN COMPLEX WITH DU PPI AND MG IN H32 DBREF 4AOZ A 1 144 UNP O31801 YNCF_BACSU 1 144 DBREF 4AOZ B 1 144 UNP O31801 YNCF_BACSU 1 144 DBREF 4AOZ C 1 144 UNP O31801 YNCF_BACSU 1 144 SEQRES 1 A 144 MET THR MET GLN ILE LYS ILE LYS TYR LEU ASP GLU THR SEQRES 2 A 144 GLN THR ARG ILE SER LYS ILE GLU GLN GLY ASP TRP ILE SEQRES 3 A 144 ASP LEU ARG ALA ALA GLU ASP VAL THR ILE LYS LYS ASP SEQRES 4 A 144 GLU PHE LYS LEU VAL PRO LEU GLY VAL ALA MET GLU LEU SEQRES 5 A 144 PRO GLU GLY TYR GLU ALA HIS VAL VAL PRO ARG SER SER SEQRES 6 A 144 THR TYR LYS ASN PHE GLY VAL ILE GLN THR ASN SER MET SEQRES 7 A 144 GLY VAL ILE ASP GLU SER TYR LYS GLY ASP ASN ASP PHE SEQRES 8 A 144 TRP PHE PHE PRO ALA TYR ALA LEU ARG ASP THR GLU ILE SEQRES 9 A 144 LYS LYS GLY ASP ARG ILE CYS GLN PHE ARG ILE MET LYS SEQRES 10 A 144 LYS MET PRO ALA VAL GLU LEU VAL GLU VAL GLU HIS LEU SEQRES 11 A 144 GLY ASN GLU ASP ARG GLY GLY LEU GLY SER THR GLY THR SEQRES 12 A 144 LYS SEQRES 1 B 144 MET THR MET GLN ILE LYS ILE LYS TYR LEU ASP GLU THR SEQRES 2 B 144 GLN THR ARG ILE SER LYS ILE GLU GLN GLY ASP TRP ILE SEQRES 3 B 144 ASP LEU ARG ALA ALA GLU ASP VAL THR ILE LYS LYS ASP SEQRES 4 B 144 GLU PHE LYS LEU VAL PRO LEU GLY VAL ALA MET GLU LEU SEQRES 5 B 144 PRO GLU GLY TYR GLU ALA HIS VAL VAL PRO ARG SER SER SEQRES 6 B 144 THR TYR LYS ASN PHE GLY VAL ILE GLN THR ASN SER MET SEQRES 7 B 144 GLY VAL ILE ASP GLU SER TYR LYS GLY ASP ASN ASP PHE SEQRES 8 B 144 TRP PHE PHE PRO ALA TYR ALA LEU ARG ASP THR GLU ILE SEQRES 9 B 144 LYS LYS GLY ASP ARG ILE CYS GLN PHE ARG ILE MET LYS SEQRES 10 B 144 LYS MET PRO ALA VAL GLU LEU VAL GLU VAL GLU HIS LEU SEQRES 11 B 144 GLY ASN GLU ASP ARG GLY GLY LEU GLY SER THR GLY THR SEQRES 12 B 144 LYS SEQRES 1 C 144 MET THR MET GLN ILE LYS ILE LYS TYR LEU ASP GLU THR SEQRES 2 C 144 GLN THR ARG ILE SER LYS ILE GLU GLN GLY ASP TRP ILE SEQRES 3 C 144 ASP LEU ARG ALA ALA GLU ASP VAL THR ILE LYS LYS ASP SEQRES 4 C 144 GLU PHE LYS LEU VAL PRO LEU GLY VAL ALA MET GLU LEU SEQRES 5 C 144 PRO GLU GLY TYR GLU ALA HIS VAL VAL PRO ARG SER SER SEQRES 6 C 144 THR TYR LYS ASN PHE GLY VAL ILE GLN THR ASN SER MET SEQRES 7 C 144 GLY VAL ILE ASP GLU SER TYR LYS GLY ASP ASN ASP PHE SEQRES 8 C 144 TRP PHE PHE PRO ALA TYR ALA LEU ARG ASP THR GLU ILE SEQRES 9 C 144 LYS LYS GLY ASP ARG ILE CYS GLN PHE ARG ILE MET LYS SEQRES 10 C 144 LYS MET PRO ALA VAL GLU LEU VAL GLU VAL GLU HIS LEU SEQRES 11 C 144 GLY ASN GLU ASP ARG GLY GLY LEU GLY SER THR GLY THR SEQRES 12 C 144 LYS HET DUR A1132 16 HET DUR B1145 16 HET POP B1146 9 HET MG B1147 1 HET ACT C1145 4 HET ACT C1146 4 HET CL C1147 1 HET DUR C1148 16 HET POP C1149 9 HET MG C1150 1 HETNAM DUR 2'-DEOXYURIDINE HETNAM POP PYROPHOSPHATE 2- HETNAM MG MAGNESIUM ION HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION FORMUL 4 DUR 3(C9 H12 N2 O5) FORMUL 6 POP 2(H2 O7 P2 2-) FORMUL 7 MG 2(MG 2+) FORMUL 8 ACT 2(C2 H3 O2 1-) FORMUL 10 CL CL 1- FORMUL 14 HOH *566(H2 O) HELIX 1 1 SER A 65 GLY A 71 1 7 HELIX 2 2 SER B 65 GLY B 71 1 7 HELIX 3 3 SER C 65 GLY C 71 1 7 SHEET 1 AA 3 VAL A 48 GLU A 51 0 SHEET 2 AA 3 MET A 3 TYR A 9 -1 O LYS A 6 N GLU A 51 SHEET 3 AA 3 VAL C 122 GLU C 126 1 O GLU C 123 N ILE A 5 SHEET 1 AB 4 ILE A 26 ARG A 29 0 SHEET 2 AB 4 ARG A 109 LYS A 117 -1 N ILE A 110 O LEU A 28 SHEET 3 AB 4 TYR A 56 PRO A 62 -1 O GLU A 57 N MET A 116 SHEET 4 AB 4 GLY A 79 ILE A 81 -1 O GLY A 79 N VAL A 60 SHEET 1 AC 2 VAL A 34 ILE A 36 0 SHEET 2 AC 2 THR A 102 ILE A 104 -1 O THR A 102 N ILE A 36 SHEET 1 AD 3 PHE A 41 PRO A 45 0 SHEET 2 AD 3 PHE A 93 ALA A 98 -1 O PHE A 94 N VAL A 44 SHEET 3 AD 3 VAL A 72 GLN A 74 -1 O ILE A 73 N TYR A 97 SHEET 1 AE 3 VAL A 122 GLU A 126 0 SHEET 2 AE 3 MET B 3 TYR B 9 1 O MET B 3 N GLU A 123 SHEET 3 AE 3 VAL B 48 GLU B 51 -1 O ALA B 49 N LYS B 8 SHEET 1 BA 4 ILE B 26 ARG B 29 0 SHEET 2 BA 4 ARG B 109 LYS B 117 -1 N ILE B 110 O LEU B 28 SHEET 3 BA 4 TYR B 56 PRO B 62 -1 O GLU B 57 N MET B 116 SHEET 4 BA 4 GLY B 79 ASP B 82 -1 O GLY B 79 N VAL B 60 SHEET 1 BB 2 VAL B 34 ILE B 36 0 SHEET 2 BB 2 THR B 102 ILE B 104 -1 O THR B 102 N ILE B 36 SHEET 1 BC 3 GLU B 40 PRO B 45 0 SHEET 2 BC 3 PHE B 93 ALA B 98 -1 O PHE B 94 N VAL B 44 SHEET 3 BC 3 VAL B 72 GLN B 74 -1 O ILE B 73 N TYR B 97 SHEET 1 BD 3 VAL B 122 GLU B 126 0 SHEET 2 BD 3 MET C 3 TYR C 9 1 O MET C 3 N GLU B 123 SHEET 3 BD 3 VAL C 48 GLU C 51 -1 O ALA C 49 N LYS C 8 SHEET 1 CA 4 ILE C 26 ARG C 29 0 SHEET 2 CA 4 ARG C 109 LYS C 117 -1 N ILE C 110 O LEU C 28 SHEET 3 CA 4 TYR C 56 PRO C 62 -1 O GLU C 57 N MET C 116 SHEET 4 CA 4 GLY C 79 ILE C 81 -1 O GLY C 79 N VAL C 60 SHEET 1 CB 2 VAL C 34 ILE C 36 0 SHEET 2 CB 2 THR C 102 ILE C 104 -1 O THR C 102 N ILE C 36 SHEET 1 CC 3 PHE C 41 PRO C 45 0 SHEET 2 CC 3 PHE C 93 ALA C 98 -1 O PHE C 94 N VAL C 44 SHEET 3 CC 3 VAL C 72 GLN C 74 -1 O ILE C 73 N TYR C 97 LINK O HOH A2075 MG MG B1147 1555 1555 2.09 LINK O HOH A2076 MG MG B1147 1555 1555 1.99 LINK O HOH A2156 MG MG C1150 1555 1555 2.08 LINK O HOH A2183 MG MG B1147 1555 1555 2.00 LINK O2 POP B1146 MG MG B1147 1555 1555 2.02 LINK O5 POP B1146 MG MG B1147 1555 1555 2.10 LINK MG MG B1147 O HOH B2172 1555 1555 2.10 LINK O HOH B2052 MG MG C1150 1555 1555 2.21 LINK O HOH B2053 MG MG C1150 1555 1555 2.09 LINK O2 POP C1149 MG MG C1150 1555 1555 2.04 LINK O5 POP C1149 MG MG C1150 1555 1555 2.05 LINK MG MG C1150 O HOH C2160 1555 1555 2.23 SITE 1 AC1 6 LEU B 43 ASN B 76 HIS B 129 DUR B1145 SITE 2 AC1 6 SER C 64 HOH C2096 SITE 1 AC2 7 PRO C 45 LEU C 46 GLY C 47 VAL C 48 SITE 2 AC2 7 PHE C 91 TRP C 92 HOH C2171 SITE 1 AC3 2 HIS B 59 HIS C 59 SITE 1 AC4 15 ASN A 76 GLY A 79 VAL A 80 ILE A 81 SITE 2 AC4 15 ASP A 82 TYR A 85 TRP A 92 PHE A 93 SITE 3 AC4 15 PRO A 95 HOH A2154 HOH A2156 SER B 64 SITE 4 AC4 15 GLY C 137 LEU C 138 POP C1149 SITE 1 AC5 12 ASN B 76 GLY B 79 VAL B 80 ILE B 81 SITE 2 AC5 12 TYR B 85 TRP B 92 PHE B 93 HIS B 129 SITE 3 AC5 12 HOH B2122 HOH B2181 SER C 64 ACT C1145 SITE 1 AC6 15 SER A 64 HOH A2184 ARG B 135 GLY B 137 SITE 2 AC6 15 LEU B 138 POP B1146 ASN C 76 GLY C 79 SITE 3 AC6 15 VAL C 80 ILE C 81 ASP C 82 TYR C 85 SITE 4 AC6 15 TRP C 92 PHE C 93 PRO C 95 SITE 1 AC7 13 DUR A1132 HOH A2156 ARG B 63 SER B 64 SITE 2 AC7 13 SER B 65 HOH B2052 HOH B2053 ARG C 135 SITE 3 AC7 13 GLY C 137 GLY C 139 SER C 140 THR C 141 SITE 4 AC7 13 MG C1150 SITE 1 AC8 14 ARG A 63 SER A 64 SER A 65 HOH A2075 SITE 2 AC8 14 HOH A2076 HOH A2183 ARG B 135 GLY B 137 SITE 3 AC8 14 LEU B 138 GLY B 139 SER B 140 THR B 141 SITE 4 AC8 14 MG B1147 DUR C1148 SITE 1 AC9 5 HOH A2156 HOH B2052 HOH B2053 POP C1149 SITE 2 AC9 5 HOH C2160 SITE 1 BC1 5 HOH A2075 HOH A2076 HOH A2183 POP B1146 SITE 2 BC1 5 HOH B2172 CRYST1 70.270 71.534 92.299 90.00 90.00 90.00 P 21 21 21 12 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 0.014231 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013979 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010834 0.00000