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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
