HEADER HYDROLASE 08-NOV-10 2XX6 TITLE STRUCTURE OF THE BACILLUS SUBTILIS PROPHAGE DUTPASE, YOSS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE COMPND 3 NUCLEOTIDOHYDROLASE YOSS; COMPND 4 CHAIN: A, B, C, D; 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; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: B834 KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.GARCIA-NAFRIA,M.HARKIOLAKI,R.PERSSON,M.J.FOGG,K.S.WILSON REVDAT 3 20-DEC-23 2XX6 1 REMARK REVDAT 2 23-MAR-11 2XX6 1 JRNL REVDAT 1 23-FEB-11 2XX6 0 JRNL AUTH J.GARCIA-NAFRIA,M.HARKIOLAKI,R.PERSSON,M.J.FOGG,K.S.WILSON JRNL TITL THE STRUCTURE OF BACILLUS SUBTILIS SP BETA PROPHAGE DUTPASE JRNL TITL 2 AND ITS COMPLEXES WITH TWO NUCLEOTIDES JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 67 167 2011 JRNL REFN ISSN 0907-4449 JRNL PMID 21358047 JRNL DOI 10.1107/S0907444911003234 REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 49805 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2678 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) : 1.74 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.79 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3545 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 195 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4077 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 477 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.79000 REMARK 3 B22 (A**2) : -0.79000 REMARK 3 B33 (A**2) : 1.18000 REMARK 3 B12 (A**2) : -0.39000 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): 0.115 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.117 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.076 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.263 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4145 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2928 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5590 ; 1.910 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7101 ; 0.993 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 504 ; 6.598 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 197 ;32.819 ;24.213 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 770 ;15.515 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;14.515 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 610 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4545 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 844 ; 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): 2507 ; 1.198 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1012 ; 0.420 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4066 ; 2.034 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1638 ; 3.322 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1520 ; 5.095 ; 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 : 4 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 1 A 128 REMARK 3 ORIGIN FOR THE GROUP (A): 7.9097 19.9696 1.3382 REMARK 3 T TENSOR REMARK 3 T11: 0.0458 T22: 0.0067 REMARK 3 T33: 0.0257 T12: 0.0034 REMARK 3 T13: -0.0240 T23: 0.0048 REMARK 3 L TENSOR REMARK 3 L11: 1.2869 L22: 1.2189 REMARK 3 L33: 1.0059 L12: -0.3681 REMARK 3 L13: -0.1549 L23: 0.1641 REMARK 3 S TENSOR REMARK 3 S11: 0.0066 S12: -0.0478 S13: -0.1140 REMARK 3 S21: 0.0030 S22: 0.0166 S23: -0.0191 REMARK 3 S31: 0.1208 S32: 0.0707 S33: -0.0233 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 128 REMARK 3 ORIGIN FOR THE GROUP (A): 7.6827 40.4628 -4.6238 REMARK 3 T TENSOR REMARK 3 T11: 0.0175 T22: 0.0121 REMARK 3 T33: 0.0171 T12: 0.0035 REMARK 3 T13: -0.0006 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 0.6232 L22: 1.2961 REMARK 3 L33: 0.6409 L12: 0.1753 REMARK 3 L13: -0.0829 L23: -0.0841 REMARK 3 S TENSOR REMARK 3 S11: -0.0010 S12: 0.0697 S13: 0.0748 REMARK 3 S21: -0.0830 S22: 0.0057 S23: -0.0585 REMARK 3 S31: -0.0265 S32: 0.0288 S33: -0.0047 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 128 REMARK 3 ORIGIN FOR THE GROUP (A): -9.6317 31.6595 3.1652 REMARK 3 T TENSOR REMARK 3 T11: 0.0386 T22: 0.0586 REMARK 3 T33: 0.0587 T12: 0.0103 REMARK 3 T13: -0.0118 T23: -0.0152 REMARK 3 L TENSOR REMARK 3 L11: 1.1468 L22: 1.2885 REMARK 3 L33: 0.7131 L12: 0.2622 REMARK 3 L13: -0.1993 L23: 0.1264 REMARK 3 S TENSOR REMARK 3 S11: 0.0344 S12: -0.0183 S13: 0.0067 REMARK 3 S21: 0.0159 S22: -0.0935 S23: 0.2191 REMARK 3 S31: 0.0016 S32: -0.1628 S33: 0.0591 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 128 REMARK 3 ORIGIN FOR THE GROUP (A): 39.5977 28.4160 -1.6945 REMARK 3 T TENSOR REMARK 3 T11: 0.0492 T22: 0.0618 REMARK 3 T33: 0.0592 T12: -0.0023 REMARK 3 T13: -0.0063 T23: 0.0104 REMARK 3 L TENSOR REMARK 3 L11: 2.0221 L22: 1.4084 REMARK 3 L33: 0.6347 L12: -0.2622 REMARK 3 L13: -0.4306 L23: -0.0907 REMARK 3 S TENSOR REMARK 3 S11: 0.0004 S12: 0.0594 S13: -0.1033 REMARK 3 S21: -0.0106 S22: 0.0115 S23: 0.2809 REMARK 3 S31: -0.0082 S32: -0.0659 S33: -0.0119 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. ARG61 FROM CHAIN B SHOWS BOND ANGLES OUT OF THE RANGE REMARK 3 BUT ELECTRON DENSITY IS CLEAR FOR THAT REGION AND GEOMETRY IS AS REMARK 3 SEEN. REMARK 4 REMARK 4 2XX6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1290046011. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52906 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 REMARK 200 RESOLUTION RANGE LOW (A) : 88.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.45000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1DUT REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M IMIDAZOLEMALATE BUFFER PH 5.5, REMARK 280 30% (V/V) PEG600 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 43.08700 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 43.08700 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 43.08700 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: 8310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.8 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 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: 7920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 BIOMT1 2 -0.500000 0.866025 0.000000 51.38150 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 88.99537 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 102.76300 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 GLY A 129 REMARK 465 ASN A 130 REMARK 465 GLY A 131 REMARK 465 ASP A 132 REMARK 465 ARG A 133 REMARK 465 GLY A 134 REMARK 465 GLY A 135 REMARK 465 HIS A 136 REMARK 465 GLY A 137 REMARK 465 SER A 138 REMARK 465 THR A 139 REMARK 465 GLY A 140 REMARK 465 THR A 141 REMARK 465 LYS A 142 REMARK 465 LYS B 17 REMARK 465 MET B 18 REMARK 465 GLU B 19 REMARK 465 GLN B 20 REMARK 465 GLY B 129 REMARK 465 ASN B 130 REMARK 465 GLY B 131 REMARK 465 ASP B 132 REMARK 465 ARG B 133 REMARK 465 GLY B 134 REMARK 465 GLY B 135 REMARK 465 HIS B 136 REMARK 465 GLY B 137 REMARK 465 SER B 138 REMARK 465 THR B 139 REMARK 465 GLY B 140 REMARK 465 THR B 141 REMARK 465 LYS B 142 REMARK 465 ASN C 16 REMARK 465 LYS C 17 REMARK 465 GLY C 129 REMARK 465 ASN C 130 REMARK 465 GLY C 131 REMARK 465 ASP C 132 REMARK 465 ARG C 133 REMARK 465 GLY C 134 REMARK 465 GLY C 135 REMARK 465 HIS C 136 REMARK 465 GLY C 137 REMARK 465 SER C 138 REMARK 465 THR C 139 REMARK 465 GLY C 140 REMARK 465 THR C 141 REMARK 465 LYS C 142 REMARK 465 ASN D 16 REMARK 465 LYS D 17 REMARK 465 MET D 18 REMARK 465 GLU D 19 REMARK 465 GLN D 20 REMARK 465 GLY D 129 REMARK 465 ASN D 130 REMARK 465 GLY D 131 REMARK 465 ASP D 132 REMARK 465 ARG D 133 REMARK 465 GLY D 134 REMARK 465 GLY D 135 REMARK 465 HIS D 136 REMARK 465 GLY D 137 REMARK 465 SER D 138 REMARK 465 THR D 139 REMARK 465 GLY D 140 REMARK 465 THR D 141 REMARK 465 LYS D 142 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 17 CD CE NZ REMARK 480 LYS A 35 CD CE NZ REMARK 480 ASN A 87 CG OD1 ND2 REMARK 480 LYS A 103 CD CE NZ REMARK 480 LYS A 115 CE NZ REMARK 480 ARG A 127 NE CZ NH1 NH2 REMARK 480 LYS B 35 CD CE NZ REMARK 480 LYS B 103 CD CE NZ REMARK 480 LYS B 115 CE NZ REMARK 480 ARG B 127 CD NE CZ NH1 NH2 REMARK 480 MET C 18 SD CE REMARK 480 LYS C 40 CD CE NZ REMARK 480 GLU C 52 CD OE1 OE2 REMARK 480 LYS C 103 CD CE NZ REMARK 480 LYS D 66 CD CE NZ REMARK 480 LYS D 103 CG CD CE NZ REMARK 480 ARG D 107 NH1 NH2 REMARK 480 LYS D 115 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG B 61 CB ARG B 61 CG -0.194 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 61 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG B 61 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 75 -70.05 67.01 REMARK 500 SER B 75 -65.02 67.74 REMARK 500 SER C 75 -74.15 65.59 REMARK 500 SER D 75 -74.65 65.92 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 A2018 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH B2010 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH B2033 DISTANCE = 6.96 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BAZ RELATED DB: PDB REMARK 900 STRUCTURE OF YOSS, A PUTATIVE DUTPASE FROM BACILLUS SUBTILIS DBREF 2XX6 A 1 142 UNP O34919 YOSS_BACSU 1 142 DBREF 2XX6 B 1 142 UNP O34919 YOSS_BACSU 1 142 DBREF 2XX6 C 1 142 UNP O34919 YOSS_BACSU 1 142 DBREF 2XX6 D 1 142 UNP O34919 YOSS_BACSU 1 142 SEQRES 1 A 142 MET GLN ILE LYS ILE LYS TYR LEU ASP GLU THR GLN THR SEQRES 2 A 142 ARG ILE ASN LYS MET GLU GLN GLY ASP TRP ILE ASP LEU SEQRES 3 A 142 ARG ALA ALA GLU ASP VAL ALA ILE LYS LYS ASP GLU PHE SEQRES 4 A 142 LYS LEU VAL PRO LEU GLY VAL ALA MET GLU LEU PRO GLU SEQRES 5 A 142 GLY TYR GLU ALA HIS VAL VAL PRO ARG SER SER THR TYR SEQRES 6 A 142 LYS ASN PHE GLY VAL ILE GLN THR ASN SER MET GLY VAL SEQRES 7 A 142 ILE ASP GLU SER TYR LYS GLY ASP ASN ASP PHE TRP PHE SEQRES 8 A 142 PHE PRO ALA TYR ALA LEU ARG ASP THR LYS ILE LYS LYS SEQRES 9 A 142 GLY ASP ARG ILE CYS GLN PHE ARG ILE MET LYS LYS MET SEQRES 10 A 142 PRO ALA VAL ASP LEU ILE GLU VAL ASP ARG LEU GLY ASN SEQRES 11 A 142 GLY ASP ARG GLY GLY HIS GLY SER THR GLY THR LYS SEQRES 1 B 142 MET GLN ILE LYS ILE LYS TYR LEU ASP GLU THR GLN THR SEQRES 2 B 142 ARG ILE ASN LYS MET GLU GLN GLY ASP TRP ILE ASP LEU SEQRES 3 B 142 ARG ALA ALA GLU ASP VAL ALA ILE LYS LYS ASP GLU PHE SEQRES 4 B 142 LYS LEU VAL PRO LEU GLY VAL ALA MET GLU LEU PRO GLU SEQRES 5 B 142 GLY TYR GLU ALA HIS VAL VAL PRO ARG SER SER THR TYR SEQRES 6 B 142 LYS ASN PHE GLY VAL ILE GLN THR ASN SER MET GLY VAL SEQRES 7 B 142 ILE ASP GLU SER TYR LYS GLY ASP ASN ASP PHE TRP PHE SEQRES 8 B 142 PHE PRO ALA TYR ALA LEU ARG ASP THR LYS ILE LYS LYS SEQRES 9 B 142 GLY ASP ARG ILE CYS GLN PHE ARG ILE MET LYS LYS MET SEQRES 10 B 142 PRO ALA VAL ASP LEU ILE GLU VAL ASP ARG LEU GLY ASN SEQRES 11 B 142 GLY ASP ARG GLY GLY HIS GLY SER THR GLY THR LYS SEQRES 1 C 142 MET GLN ILE LYS ILE LYS TYR LEU ASP GLU THR GLN THR SEQRES 2 C 142 ARG ILE ASN LYS MET GLU GLN GLY ASP TRP ILE ASP LEU SEQRES 3 C 142 ARG ALA ALA GLU ASP VAL ALA ILE LYS LYS ASP GLU PHE SEQRES 4 C 142 LYS LEU VAL PRO LEU GLY VAL ALA MET GLU LEU PRO GLU SEQRES 5 C 142 GLY TYR GLU ALA HIS VAL VAL PRO ARG SER SER THR TYR SEQRES 6 C 142 LYS ASN PHE GLY VAL ILE GLN THR ASN SER MET GLY VAL SEQRES 7 C 142 ILE ASP GLU SER TYR LYS GLY ASP ASN ASP PHE TRP PHE SEQRES 8 C 142 PHE PRO ALA TYR ALA LEU ARG ASP THR LYS ILE LYS LYS SEQRES 9 C 142 GLY ASP ARG ILE CYS GLN PHE ARG ILE MET LYS LYS MET SEQRES 10 C 142 PRO ALA VAL ASP LEU ILE GLU VAL ASP ARG LEU GLY ASN SEQRES 11 C 142 GLY ASP ARG GLY GLY HIS GLY SER THR GLY THR LYS SEQRES 1 D 142 MET GLN ILE LYS ILE LYS TYR LEU ASP GLU THR GLN THR SEQRES 2 D 142 ARG ILE ASN LYS MET GLU GLN GLY ASP TRP ILE ASP LEU SEQRES 3 D 142 ARG ALA ALA GLU ASP VAL ALA ILE LYS LYS ASP GLU PHE SEQRES 4 D 142 LYS LEU VAL PRO LEU GLY VAL ALA MET GLU LEU PRO GLU SEQRES 5 D 142 GLY TYR GLU ALA HIS VAL VAL PRO ARG SER SER THR TYR SEQRES 6 D 142 LYS ASN PHE GLY VAL ILE GLN THR ASN SER MET GLY VAL SEQRES 7 D 142 ILE ASP GLU SER TYR LYS GLY ASP ASN ASP PHE TRP PHE SEQRES 8 D 142 PHE PRO ALA TYR ALA LEU ARG ASP THR LYS ILE LYS LYS SEQRES 9 D 142 GLY ASP ARG ILE CYS GLN PHE ARG ILE MET LYS LYS MET SEQRES 10 D 142 PRO ALA VAL ASP LEU ILE GLU VAL ASP ARG LEU GLY ASN SEQRES 11 D 142 GLY ASP ARG GLY GLY HIS GLY SER THR GLY THR LYS FORMUL 5 HOH *477(H2 O) HELIX 1 1 SER A 63 GLY A 69 1 7 HELIX 2 2 SER B 63 GLY B 69 1 7 HELIX 3 3 SER C 63 GLY C 69 1 7 HELIX 4 4 SER D 63 GLY D 69 1 7 SHEET 1 AA 4 LYS A 17 GLN A 20 0 SHEET 2 AA 4 VAL B 120 GLU B 124 -1 O VAL B 120 N GLN A 20 SHEET 3 AA 4 GLN A 2 TYR A 7 1 O ILE A 3 N ILE B 123 SHEET 4 AA 4 VAL A 46 GLU A 49 -1 O ALA A 47 N LYS A 6 SHEET 1 AB 4 ILE A 24 ARG A 27 0 SHEET 2 AB 4 ARG A 107 LYS A 115 -1 N ILE A 108 O LEU A 26 SHEET 3 AB 4 TYR A 54 PRO A 60 -1 O GLU A 55 N MET A 114 SHEET 4 AB 4 GLY A 77 ASP A 80 -1 O GLY A 77 N VAL A 58 SHEET 1 AC 2 VAL A 32 ILE A 34 0 SHEET 2 AC 2 THR A 100 ILE A 102 -1 O THR A 100 N ILE A 34 SHEET 1 AD 3 PHE A 39 PRO A 43 0 SHEET 2 AD 3 PHE A 91 ALA A 96 -1 O PHE A 92 N VAL A 42 SHEET 3 AD 3 VAL A 70 GLN A 72 -1 O ILE A 71 N TYR A 95 SHEET 1 AE 3 ASP A 121 GLU A 124 0 SHEET 2 AE 3 GLN C 2 TYR C 7 1 O ILE C 3 N ILE A 123 SHEET 3 AE 3 VAL C 46 GLU C 49 -1 O ALA C 47 N LYS C 6 SHEET 1 BA 5 VAL B 70 GLN B 72 0 SHEET 2 BA 5 PHE B 89 ALA B 96 -1 O TYR B 95 N ILE B 71 SHEET 3 BA 5 PHE B 39 GLU B 49 -1 O LYS B 40 N ALA B 94 SHEET 4 BA 5 GLN B 2 TYR B 7 -1 O LYS B 4 N GLU B 49 SHEET 5 BA 5 ASP C 121 GLU C 124 1 O ASP C 121 N ILE B 3 SHEET 1 BB 4 ILE B 24 ARG B 27 0 SHEET 2 BB 4 ARG B 107 LYS B 115 -1 N ILE B 108 O LEU B 26 SHEET 3 BB 4 TYR B 54 PRO B 60 -1 O GLU B 55 N MET B 114 SHEET 4 BB 4 GLY B 77 ASP B 80 -1 O GLY B 77 N VAL B 58 SHEET 1 BC 2 VAL B 32 ILE B 34 0 SHEET 2 BC 2 THR B 100 ILE B 102 -1 O THR B 100 N ILE B 34 SHEET 1 CA 4 ILE C 24 ARG C 27 0 SHEET 2 CA 4 ARG C 107 LYS C 115 -1 N ILE C 108 O LEU C 26 SHEET 3 CA 4 TYR C 54 PRO C 60 -1 O GLU C 55 N MET C 114 SHEET 4 CA 4 GLY C 77 ASP C 80 -1 O GLY C 77 N VAL C 58 SHEET 1 CB 2 VAL C 32 ILE C 34 0 SHEET 2 CB 2 THR C 100 ILE C 102 -1 O THR C 100 N ILE C 34 SHEET 1 CC 3 PHE C 39 PRO C 43 0 SHEET 2 CC 3 PHE C 91 ALA C 96 -1 O PHE C 92 N VAL C 42 SHEET 3 CC 3 VAL C 70 GLN C 72 -1 O ILE C 71 N TYR C 95 SHEET 1 DA 4 LYS D 4 TYR D 7 0 SHEET 2 DA 4 PHE D 39 GLU D 49 -1 O ALA D 47 N LYS D 6 SHEET 3 DA 4 PHE D 89 ALA D 96 -1 O TRP D 90 N LEU D 44 SHEET 4 DA 4 VAL D 70 GLN D 72 -1 O ILE D 71 N TYR D 95 SHEET 1 DB 4 ILE D 24 ARG D 27 0 SHEET 2 DB 4 ARG D 107 LYS D 115 -1 N ILE D 108 O LEU D 26 SHEET 3 DB 4 TYR D 54 PRO D 60 -1 O GLU D 55 N MET D 114 SHEET 4 DB 4 GLY D 77 ASP D 80 -1 O GLY D 77 N VAL D 58 SHEET 1 DC 2 VAL D 32 ILE D 34 0 SHEET 2 DC 2 THR D 100 ILE D 102 -1 O THR D 100 N ILE D 34 CRYST1 102.763 102.763 86.174 90.00 90.00 120.00 P 63 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 0.009731 0.005618 0.000000 0.00000 SCALE2 0.000000 0.011237 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011604 0.00000