HEADER HYDROLASE 22-APR-10 2XCD TITLE STRUCTURE OF YNCF,THE GENOMIC DUTPASE FROM BACILLUS SUBTILIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE COMPND 3 YNCF; COMPND 4 CHAIN: A, B, C, D, E, F; COMPND 5 SYNONYM: YNCF, 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; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: B834(DE3) KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.GARCIA,L.BURCHELL,M.TAKEZAWA,N.J.RZECHORZEK,M.FOGG,K.S.WILSON REVDAT 4 20-DEC-23 2XCD 1 REMARK LINK REVDAT 3 11-APR-12 2XCD 1 JRNL REMARK VERSN HETSYN REVDAT 2 25-AUG-10 2XCD 1 JRNL REVDAT 1 11-AUG-10 2XCD 0 JRNL AUTH J.GARCIA-NAFRIA,L.BURCHELL,M.TAKEZAWA,N.J.RZECHORZEK,M.FOGG, JRNL AUTH 2 K.S.WILSON JRNL TITL THE STRUCTURE OF THE GENOMIC BACILLUS SUBTILIS DUTPASE: JRNL TITL 2 NOVEL FEATURES IN THE PHE-LID. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 66 953 2010 JRNL REFN ISSN 0907-4449 JRNL PMID 20823546 JRNL DOI 10.1107/S0907444910026272 REMARK 2 REMARK 2 RESOLUTION. 1.84 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) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 76855 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) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3988 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) : 1.84 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.89 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4929 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.1720 REMARK 3 BIN FREE R VALUE SET COUNT : 279 REMARK 3 BIN FREE R VALUE : 0.2440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6292 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.16000 REMARK 3 B22 (A**2) : -0.65000 REMARK 3 B33 (A**2) : 1.82000 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): 0.024 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.023 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.243 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6524 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8809 ; 1.424 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 794 ; 6.692 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 315 ;34.407 ;24.857 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1242 ;16.686 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;15.771 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 960 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4888 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 3905 ; 0.693 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6364 ; 1.168 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2619 ; 1.987 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2437 ; 3.031 ; 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 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 3 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.511 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : K, -L, -H REMARK 3 TWIN FRACTION : 0.310 REMARK 3 TWIN DOMAIN : 3 REMARK 3 TWIN OPERATOR : -L, -H, K REMARK 3 TWIN FRACTION : 0.178 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 REMARK 4 REMARK 4 2XCD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-APR-10. REMARK 100 THE DEPOSITION ID IS D_1290043688. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81408 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 31.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.88000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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 2BAZ REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MGCL2,28% PEG 550, 0.1M HEPES PH REMARK 280 7.5 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 49.40500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.55500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.42000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.55500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 49.40500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.42000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 9310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -101.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F 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 350 REMARK 350 BIOMOLECULE: 2 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: 9740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -113.7 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 GLY A 131 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 GLY B 131 REMARK 465 ASN B 132 REMARK 465 GLU B 133 REMARK 465 ASP B 134 REMARK 465 ARG B 135 REMARK 465 GLY B 136 REMARK 465 GLY B 137 REMARK 465 LEU B 138 REMARK 465 GLY B 139 REMARK 465 SER B 140 REMARK 465 THR B 141 REMARK 465 GLY B 142 REMARK 465 THR B 143 REMARK 465 LYS B 144 REMARK 465 MET C 1 REMARK 465 GLY C 131 REMARK 465 ASN C 132 REMARK 465 GLU C 133 REMARK 465 ASP C 134 REMARK 465 ARG C 135 REMARK 465 GLY C 136 REMARK 465 GLY C 137 REMARK 465 LEU C 138 REMARK 465 GLY C 139 REMARK 465 SER C 140 REMARK 465 THR C 141 REMARK 465 GLY C 142 REMARK 465 THR C 143 REMARK 465 LYS C 144 REMARK 465 MET D 1 REMARK 465 GLY D 131 REMARK 465 ASN D 132 REMARK 465 GLU D 133 REMARK 465 ASP D 134 REMARK 465 ARG D 135 REMARK 465 GLY D 136 REMARK 465 GLY D 137 REMARK 465 LEU D 138 REMARK 465 GLY D 139 REMARK 465 SER D 140 REMARK 465 THR D 141 REMARK 465 GLY D 142 REMARK 465 THR D 143 REMARK 465 LYS D 144 REMARK 465 MET E 1 REMARK 465 GLY E 131 REMARK 465 ASN E 132 REMARK 465 GLU E 133 REMARK 465 ASP E 134 REMARK 465 ARG E 135 REMARK 465 GLY E 136 REMARK 465 GLY E 137 REMARK 465 LEU E 138 REMARK 465 GLY E 139 REMARK 465 SER E 140 REMARK 465 THR E 141 REMARK 465 GLY E 142 REMARK 465 THR E 143 REMARK 465 LYS E 144 REMARK 465 MET F 1 REMARK 465 GLY F 131 REMARK 465 ASN F 132 REMARK 465 GLU F 133 REMARK 465 ASP F 134 REMARK 465 ARG F 135 REMARK 465 GLY F 136 REMARK 465 GLY F 137 REMARK 465 LEU F 138 REMARK 465 GLY F 139 REMARK 465 SER F 140 REMARK 465 THR F 141 REMARK 465 GLY F 142 REMARK 465 THR F 143 REMARK 465 LYS F 144 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 B 19 CB CG CD CE NZ REMARK 470 LYS F 6 CD CE NZ 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 -71.06 63.44 REMARK 500 SER B 77 -74.80 63.75 REMARK 500 SER C 77 -79.58 61.24 REMARK 500 SER D 77 -67.92 59.28 REMARK 500 SER E 77 -74.00 66.76 REMARK 500 SER F 77 -68.87 66.38 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 NA E1132 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 109 NH2 REMARK 620 2 HOH A2099 O 129.0 REMARK 620 3 THR E 15 OG1 131.6 61.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA D1131 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C2106 O REMARK 620 2 THR D 15 OG1 63.7 REMARK 620 3 HOH D2014 O 102.9 83.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA F1132 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER F 65 OG REMARK 620 2 HOH F2075 O 148.6 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 NA A 1131 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 146 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL C 1131 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA C 1132 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 1133 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA D 1131 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG E 1131 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL E 145 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA E 1132 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL F 1131 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA F 1132 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1131 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XCE RELATED DB: PDB REMARK 900 STRUCTURE OF YNCF IN COMPLEX WITH DUPNHPP DBREF 2XCD A 1 144 UNP O31801 YNCF_BACSU 1 144 DBREF 2XCD B 1 144 UNP O31801 YNCF_BACSU 1 144 DBREF 2XCD C 1 144 UNP O31801 YNCF_BACSU 1 144 DBREF 2XCD D 1 144 UNP O31801 YNCF_BACSU 1 144 DBREF 2XCD E 1 144 UNP O31801 YNCF_BACSU 1 144 DBREF 2XCD F 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 SEQRES 1 D 144 MET THR MET GLN ILE LYS ILE LYS TYR LEU ASP GLU THR SEQRES 2 D 144 GLN THR ARG ILE SER LYS ILE GLU GLN GLY ASP TRP ILE SEQRES 3 D 144 ASP LEU ARG ALA ALA GLU ASP VAL THR ILE LYS LYS ASP SEQRES 4 D 144 GLU PHE LYS LEU VAL PRO LEU GLY VAL ALA MET GLU LEU SEQRES 5 D 144 PRO GLU GLY TYR GLU ALA HIS VAL VAL PRO ARG SER SER SEQRES 6 D 144 THR TYR LYS ASN PHE GLY VAL ILE GLN THR ASN SER MET SEQRES 7 D 144 GLY VAL ILE ASP GLU SER TYR LYS GLY ASP ASN ASP PHE SEQRES 8 D 144 TRP PHE PHE PRO ALA TYR ALA LEU ARG ASP THR GLU ILE SEQRES 9 D 144 LYS LYS GLY ASP ARG ILE CYS GLN PHE ARG ILE MET LYS SEQRES 10 D 144 LYS MET PRO ALA VAL GLU LEU VAL GLU VAL GLU HIS LEU SEQRES 11 D 144 GLY ASN GLU ASP ARG GLY GLY LEU GLY SER THR GLY THR SEQRES 12 D 144 LYS SEQRES 1 E 144 MET THR MET GLN ILE LYS ILE LYS TYR LEU ASP GLU THR SEQRES 2 E 144 GLN THR ARG ILE SER LYS ILE GLU GLN GLY ASP TRP ILE SEQRES 3 E 144 ASP LEU ARG ALA ALA GLU ASP VAL THR ILE LYS LYS ASP SEQRES 4 E 144 GLU PHE LYS LEU VAL PRO LEU GLY VAL ALA MET GLU LEU SEQRES 5 E 144 PRO GLU GLY TYR GLU ALA HIS VAL VAL PRO ARG SER SER SEQRES 6 E 144 THR TYR LYS ASN PHE GLY VAL ILE GLN THR ASN SER MET SEQRES 7 E 144 GLY VAL ILE ASP GLU SER TYR LYS GLY ASP ASN ASP PHE SEQRES 8 E 144 TRP PHE PHE PRO ALA TYR ALA LEU ARG ASP THR GLU ILE SEQRES 9 E 144 LYS LYS GLY ASP ARG ILE CYS GLN PHE ARG ILE MET LYS SEQRES 10 E 144 LYS MET PRO ALA VAL GLU LEU VAL GLU VAL GLU HIS LEU SEQRES 11 E 144 GLY ASN GLU ASP ARG GLY GLY LEU GLY SER THR GLY THR SEQRES 12 E 144 LYS SEQRES 1 F 144 MET THR MET GLN ILE LYS ILE LYS TYR LEU ASP GLU THR SEQRES 2 F 144 GLN THR ARG ILE SER LYS ILE GLU GLN GLY ASP TRP ILE SEQRES 3 F 144 ASP LEU ARG ALA ALA GLU ASP VAL THR ILE LYS LYS ASP SEQRES 4 F 144 GLU PHE LYS LEU VAL PRO LEU GLY VAL ALA MET GLU LEU SEQRES 5 F 144 PRO GLU GLY TYR GLU ALA HIS VAL VAL PRO ARG SER SER SEQRES 6 F 144 THR TYR LYS ASN PHE GLY VAL ILE GLN THR ASN SER MET SEQRES 7 F 144 GLY VAL ILE ASP GLU SER TYR LYS GLY ASP ASN ASP PHE SEQRES 8 F 144 TRP PHE PHE PRO ALA TYR ALA LEU ARG ASP THR GLU ILE SEQRES 9 F 144 LYS LYS GLY ASP ARG ILE CYS GLN PHE ARG ILE MET LYS SEQRES 10 F 144 LYS MET PRO ALA VAL GLU LEU VAL GLU VAL GLU HIS LEU SEQRES 11 F 144 GLY ASN GLU ASP ARG GLY GLY LEU GLY SER THR GLY THR SEQRES 12 F 144 LYS HET MG A 146 1 HET NA A1131 1 HET NA B1131 1 HET CL C1131 1 HET NA C1132 1 HET GOL C1133 6 HET NA D1131 1 HET CL E 145 1 HET MG E1131 1 HET NA E1132 1 HET CL F1131 1 HET NA F1132 1 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 7 MG 2(MG 2+) FORMUL 8 NA 6(NA 1+) FORMUL 10 CL 3(CL 1-) FORMUL 12 GOL C3 H8 O3 FORMUL 19 HOH *740(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 HELIX 4 4 SER D 65 GLY D 71 1 7 HELIX 5 5 SER E 65 GLY E 71 1 7 HELIX 6 6 SER F 65 GLY F 71 1 7 SHEET 1 AA 5 VAL A 72 GLN A 74 0 SHEET 2 AA 5 PHE A 91 ALA A 98 -1 O TYR A 97 N ILE A 73 SHEET 3 AA 5 PHE A 41 GLU A 51 -1 O LYS A 42 N ALA A 96 SHEET 4 AA 5 MET A 3 TYR A 9 -1 O LYS A 6 N GLU A 51 SHEET 5 AA 5 VAL B 122 GLU B 126 1 O GLU B 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 ASP A 82 -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 VAL A 122 GLU A 126 0 SHEET 2 AD 3 MET C 3 TYR C 9 1 O MET C 3 N GLU A 123 SHEET 3 AD 3 VAL C 48 GLU C 51 -1 O ALA C 49 N LYS C 8 SHEET 1 BA 3 VAL B 48 GLU B 51 0 SHEET 2 BA 3 MET B 3 TYR B 9 -1 O LYS B 6 N GLU B 51 SHEET 3 BA 3 VAL C 122 GLU C 126 1 O GLU C 123 N ILE B 5 SHEET 1 BB 4 ILE B 26 ARG B 29 0 SHEET 2 BB 4 ARG B 109 LYS B 117 -1 N ILE B 110 O LEU B 28 SHEET 3 BB 4 TYR B 56 PRO B 62 -1 O GLU B 57 N MET B 116 SHEET 4 BB 4 GLY B 79 ASP B 82 -1 O GLY B 79 N VAL B 60 SHEET 1 BC 2 VAL B 34 ILE B 36 0 SHEET 2 BC 2 THR B 102 ILE B 104 -1 O THR B 102 N ILE B 36 SHEET 1 BD 3 PHE B 41 PRO B 45 0 SHEET 2 BD 3 PHE B 93 ALA B 98 -1 O PHE B 94 N VAL B 44 SHEET 3 BD 3 VAL B 72 GLN B 74 -1 O ILE B 73 N TYR B 97 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 ASP C 82 -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 GLU C 40 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 SHEET 1 DA 3 VAL D 48 GLU D 51 0 SHEET 2 DA 3 GLN D 4 TYR D 9 -1 O LYS D 6 N GLU D 51 SHEET 3 DA 3 GLU E 123 GLU E 126 1 O GLU E 123 N ILE D 5 SHEET 1 DB 4 ILE D 26 ARG D 29 0 SHEET 2 DB 4 ARG D 109 LYS D 117 -1 O CYS D 111 N LEU D 28 SHEET 3 DB 4 TYR D 56 PRO D 62 -1 O GLU D 57 N MET D 116 SHEET 4 DB 4 GLY D 79 ASP D 82 -1 O GLY D 79 N VAL D 60 SHEET 1 DC 2 VAL D 34 ILE D 36 0 SHEET 2 DC 2 THR D 102 ILE D 104 -1 O THR D 102 N ILE D 36 SHEET 1 DD 3 PHE D 41 PRO D 45 0 SHEET 2 DD 3 PHE D 93 ALA D 98 -1 O PHE D 94 N VAL D 44 SHEET 3 DD 3 VAL D 72 GLN D 74 -1 O ILE D 73 N TYR D 97 SHEET 1 DE 3 GLU D 123 GLU D 126 0 SHEET 2 DE 3 GLN F 4 TYR F 9 1 O ILE F 5 N VAL D 125 SHEET 3 DE 3 VAL F 48 GLU F 51 -1 O ALA F 49 N LYS F 8 SHEET 1 EA 3 VAL E 48 GLU E 51 0 SHEET 2 EA 3 MET E 3 TYR E 9 -1 O LYS E 6 N GLU E 51 SHEET 3 EA 3 VAL F 122 GLU F 126 1 O GLU F 123 N ILE E 5 SHEET 1 EB 4 ILE E 26 ARG E 29 0 SHEET 2 EB 4 ARG E 109 LYS E 117 -1 O CYS E 111 N LEU E 28 SHEET 3 EB 4 TYR E 56 PRO E 62 -1 O GLU E 57 N MET E 116 SHEET 4 EB 4 GLY E 79 ASP E 82 -1 O GLY E 79 N VAL E 60 SHEET 1 EC 2 VAL E 34 ILE E 36 0 SHEET 2 EC 2 THR E 102 ILE E 104 -1 O THR E 102 N ILE E 36 SHEET 1 ED 3 PHE E 41 PRO E 45 0 SHEET 2 ED 3 PHE E 93 ALA E 98 -1 O PHE E 94 N VAL E 44 SHEET 3 ED 3 VAL E 72 GLN E 74 -1 O ILE E 73 N TYR E 97 SHEET 1 FA 4 ILE F 26 ARG F 29 0 SHEET 2 FA 4 ARG F 109 LYS F 117 -1 N ILE F 110 O LEU F 28 SHEET 3 FA 4 TYR F 56 PRO F 62 -1 O GLU F 57 N MET F 116 SHEET 4 FA 4 GLY F 79 ASP F 82 -1 O GLY F 79 N VAL F 60 SHEET 1 FB 2 VAL F 34 ILE F 36 0 SHEET 2 FB 2 THR F 102 ILE F 104 -1 O THR F 102 N ILE F 36 SHEET 1 FC 3 PHE F 41 PRO F 45 0 SHEET 2 FC 3 PHE F 93 ALA F 98 -1 O PHE F 94 N VAL F 44 SHEET 3 FC 3 VAL F 72 GLN F 74 -1 O ILE F 73 N TYR F 97 LINK OG SER A 65 NA NA A1131 1555 1555 2.95 LINK NH2 ARG A 109 NA NA E1132 4554 1555 3.08 LINK MG MG A 146 O HOH A2042 1555 1555 2.92 LINK O HOH A2099 NA NA E1132 4554 1555 3.16 LINK OG1 THR B 15 NA NA B1131 1555 1555 2.98 LINK OG SER C 65 NA NA C1132 1555 1555 2.94 LINK O HOH C2106 NA NA D1131 3554 1555 3.00 LINK OG1 THR D 15 NA NA D1131 1555 1555 3.13 LINK NA NA D1131 O HOH D2014 1555 1555 2.95 LINK OG1 THR E 15 NA NA E1132 1555 1555 3.18 LINK OG SER F 65 NA NA F1132 1555 1555 2.99 LINK NA NA F1132 O HOH F2075 1555 1555 2.91 SITE 1 AC1 2 SER A 65 LYS E 105 SITE 1 AC2 2 HOH A2042 ASP B 39 SITE 1 AC3 3 LYS C 19 ASP C 27 ARG C 109 SITE 1 AC4 2 SER C 65 LYS D 105 SITE 1 AC5 4 TYR C 85 PHE C 91 TRP C 92 PHE C 93 SITE 1 AC6 5 ARG C 109 HOH C2106 THR D 15 GLY D 107 SITE 2 AC6 5 HOH D2014 SITE 1 AC7 2 ASP E 39 HOH E2047 SITE 1 AC8 4 LYS A 19 ASP A 27 ARG A 109 HOH A2028 SITE 1 AC9 3 ARG A 109 THR E 15 GLY E 107 SITE 1 BC1 3 LYS F 19 ASP F 27 ARG F 109 SITE 1 BC2 2 SER F 65 HOH F2075 SITE 1 BC3 3 THR B 15 GLY B 107 ARG F 109 CRYST1 98.810 98.840 99.110 90.00 90.00 90.00 P 21 21 21 24 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 0.010120 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010117 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010090 0.00000