HEADER HYDROLASE 10-DEC-12 3ZEZ TITLE PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO- TITLE 2 ONCOGENIC G PROTEIN-LIKE MECHANISM.(STAPHYLOCOCCUS BACTERIOPHAGE TITLE 3 80ALPHA DUTPASE WITH DUPNHPP). COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUTPASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TRIMERIC DUTPASE; COMPND 5 EC: 3.6.1.23; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: STRUCTURE IN PRESENCE OF DUPNHPP AND MAGNESIUM SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS PHAGE 80ALPHA; SOURCE 3 ORGANISM_TAXID: 53369; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET28A KEYWDS HYDROLASE, STAPHYLOCOCCUS AUREUS, PHAGE, PATHOGENICITY ISLAND, SAPI KEYWDS 2 INDUCTION, GENE TRANSFER, MOONLIGHTING PROTEINS, DUTPASE, DUTP, G- KEYWDS 3 PROTEIN, P-LOOP EXPDTA X-RAY DIFFRACTION AUTHOR M.A.TORMO-MAS,J.DONDERIS,M.GARCIA-CABALLER,A.ALT,I.MIR-SANCHIS, AUTHOR 2 A.MARINA,J.R.PENADES REVDAT 5 20-DEC-23 3ZEZ 1 REMARK LINK REVDAT 4 17-APR-13 3ZEZ 1 REMARK SEQADV SEQRES REVDAT 3 03-APR-13 3ZEZ 1 TITLE REMARK REVDAT 2 20-MAR-13 3ZEZ 1 JRNL REVDAT 1 30-JAN-13 3ZEZ 0 JRNL AUTH M.A.TORMO-MAS,J.DONDERIS,M.GARCIA-CABALLER,A.ALT, JRNL AUTH 2 I.MIR-SANCHIS,A.MARINA,J.R.PENADES JRNL TITL PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A JRNL TITL 2 PROTO-ONCOGENIC G PROTEIN-LIKE MECHANISM. JRNL REF MOL.CELL V. 49 947 2013 JRNL REFN ISSN 1097-2765 JRNL PMID 23333307 JRNL DOI 10.1016/J.MOLCEL.2012.12.013 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.A.TORMO-MAS,I.MIR,A.SHRESTHA,S.M.TALLENT,S.CAMPOY,I.LASA, REMARK 1 AUTH 2 J.BARBE,R.P.NOVICK,G.E.CHRISTIE,J.R.PENADES REMARK 1 TITL MOONLIGHTING BACTERIOPHAGE PROTEINS DEREPRESS STAPHYLOCOCCAL REMARK 1 TITL 2 PATHOGENICITY ISLANDS. REMARK 1 REF NATURE V. 465 779 2010 REMARK 1 REFN ISSN 0028-0836 REMARK 1 PMID 20473284 REMARK 1 DOI 10.1038/NATURE09065 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 5457 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) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.000 REMARK 3 FREE R VALUE TEST SET COUNT : 477 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 397 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE SET COUNT : 43 REMARK 3 BIN FREE R VALUE : 0.3430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1309 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 64 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.40000 REMARK 3 B22 (A**2) : 8.02000 REMARK 3 B33 (A**2) : -3.62000 REMARK 3 B12 (A**2) : 4.44000 REMARK 3 B13 (A**2) : -2.19000 REMARK 3 B23 (A**2) : -5.24000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.081 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.924 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.880 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1357 ; 0.004 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1839 ; 1.021 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 168 ; 3.994 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 59 ;28.683 ;24.746 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 239 ;14.163 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;19.736 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 208 ; 0.047 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 993 ; 0.003 ; 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): 675 ; 0.576 ; 5.107 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 842 ; 1.074 ; 7.656 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 682 ; 0.388 ; 5.174 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. SIDE CHAINS WITH NO ELECTRON DENSITY ARE REFINED WITH REMARK 3 0 OCCUANCY REMARK 4 REMARK 4 3ZEZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1290055013. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9334 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 : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5949 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 44.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.75000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2HQU REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2-6% TERT-BUTANOL, 0.1M TRIS (PH 8.5), REMARK 280 30-50% MPD OR PEG400 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+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 -1.000000 0.000000 0.000000 44.32850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.32850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.32850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.32850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.32850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.32850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 44.32850 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 44.32850 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 44.32850 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 44.32850 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 44.32850 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 44.32850 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 44.32850 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 44.32850 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 44.32850 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 44.32850 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 44.32850 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 44.32850 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: 17730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -103.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 0.000000 -1.000000 0.000000 44.32850 REMARK 350 BIOMT2 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT3 2 1.000000 0.000000 0.000000 -44.32850 REMARK 350 BIOMT1 3 0.000000 0.000000 1.000000 44.32850 REMARK 350 BIOMT2 3 -1.000000 0.000000 0.000000 44.32850 REMARK 350 BIOMT3 3 0.000000 -1.000000 0.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 NI NI A1171 LIES ON A SPECIAL POSITION. REMARK 375 NI NI A1172 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2037 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2042 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2065 LIES ON A SPECIAL POSITION. 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 -33 REMARK 465 GLY A -32 REMARK 465 SER A -31 REMARK 465 SER A -30 REMARK 465 HIS A -29 REMARK 465 HIS A -28 REMARK 465 HIS A -27 REMARK 465 HIS A -26 REMARK 465 HIS A -25 REMARK 465 HIS A -24 REMARK 465 SER A -23 REMARK 465 SER A -22 REMARK 465 GLY A -21 REMARK 465 LEU A -20 REMARK 465 VAL A -19 REMARK 465 PRO A -18 REMARK 465 ARG A -17 REMARK 465 GLY A -16 REMARK 465 SER A -15 REMARK 465 HIS A -14 REMARK 465 MET A -13 REMARK 465 ALA A -12 REMARK 465 SER A -11 REMARK 465 MET A -10 REMARK 465 THR A -9 REMARK 465 GLY A -8 REMARK 465 GLY A -7 REMARK 465 GLN A -6 REMARK 465 GLN A -5 REMARK 465 MET A -4 REMARK 465 GLY A -3 REMARK 465 ARG A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 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 12 CG CD CE NZ REMARK 470 LYS A 22 CG CD CE NZ REMARK 470 PHE A 115 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 117 CG CD CE NZ REMARK 470 GLU A 118 CG CD OE1 OE2 REMARK 470 GLU A 159 CG CD OE1 OE2 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 O ILE A 114 O HOH A 2049 1.40 REMARK 500 NI NI A 1171 O HOH A 2014 1.64 REMARK 500 OD2 ASP A 81 O HOH A 2033 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2014 O HOH A 2014 6555 1.76 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 147 CG GLU A 147 CD -0.261 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 A2065 DISTANCE = 8.46 ANGSTROMS REMARK 525 HOH A2066 DISTANCE = 6.55 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 NI A1171 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 95 OD1 REMARK 620 2 ASP A 95 OD1 105.2 REMARK 620 3 ASP A 95 OD1 105.2 105.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1174 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DUP A1173 O2G REMARK 620 2 DUP A1173 O2A 68.5 REMARK 620 3 DUP A1173 O2B 66.4 86.7 REMARK 620 4 HOH A2062 O 56.4 68.8 122.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1171 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1172 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUP A 1173 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1174 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1175 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZF0 RELATED DB: PDB REMARK 900 PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO- REMARK 900 ONCOGENIC G PROTEIN-LIKE MECHANISM. ( STAPHYLOCOCCUS BACTERIOPHAGE REMARK 900 80ALPHA DUTPASE D81A MUTANT WITH DUPNHPP). REMARK 900 RELATED ID: 3ZF1 RELATED DB: PDB REMARK 900 PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO- REMARK 900 ONCOGENIC G PROTEIN-LIKE MECHANISM. ( STAPHYLOCOCCUS BACTERIOPHAGE REMARK 900 80ALPHA DUTPASE D81N MUTANT WITH DUPNHPP). REMARK 900 RELATED ID: 3ZF2 RELATED DB: PDB REMARK 900 PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO- REMARK 900 ONCOGENIC G PROTEIN-LIKE MECHANISM. ( STAPHYLOCOCCUS BACTERIOPHAGE REMARK 900 80ALPHA DUTPASE). REMARK 900 RELATED ID: 3ZF3 RELATED DB: PDB REMARK 900 PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO- REMARK 900 ONCOGENIC G PROTEIN-LIKE MECHANISM. ( STAPHYLOCOCCUS BACTERIOPHAGE REMARK 900 80ALPHA DUTPASE Y84I MUTANT). REMARK 900 RELATED ID: 3ZF4 RELATED DB: PDB REMARK 900 PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO- REMARK 900 ONCOGENIC G PROTEIN-LIKE MECHANISM. ( STAPHYLOCOCCUS BACTERIOPHAGE REMARK 900 80ALPHA DUTPASE Y81A MUTANT WITH DUPNHPP). REMARK 900 RELATED ID: 3ZF5 RELATED DB: PDB REMARK 900 PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO- REMARK 900 ONCOGENIC G PROTEIN-LIKE MECHANISM. ( STAPHYLOCOCCUS BACTERIOPHAGE REMARK 900 80ALPHA DUTPASE Y84F MUTANT WITH DUPNHPP). REMARK 900 RELATED ID: 3ZF6 RELATED DB: PDB REMARK 900 PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO- REMARK 900 ONCOGENIC G PROTEIN-LIKE MECHANISM. ( STAPHYLOCOCCUS BACTERIOPHAGE REMARK 900 80ALPHA DUTPASE D81A D110C S168C MUTANT WITH DUPNHPP). DBREF 3ZEZ A 1 170 UNP A4ZF98 A4ZF98_9CAUD 1 170 SEQADV 3ZEZ MET A -33 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ GLY A -32 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ SER A -31 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ SER A -30 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ HIS A -29 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ HIS A -28 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ HIS A -27 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ HIS A -26 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ HIS A -25 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ HIS A -24 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ SER A -23 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ SER A -22 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ GLY A -21 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ LEU A -20 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ VAL A -19 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ PRO A -18 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ ARG A -17 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ GLY A -16 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ SER A -15 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ HIS A -14 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ MET A -13 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ ALA A -12 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ SER A -11 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ MET A -10 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ THR A -9 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ GLY A -8 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ GLY A -7 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ GLN A -6 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ GLN A -5 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ MET A -4 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ GLY A -3 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ ARG A -2 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ GLY A -1 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZEZ SER A 0 UNP A4ZF98 EXPRESSION TAG SEQRES 1 A 204 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 204 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET THR GLY SEQRES 3 A 204 GLY GLN GLN MET GLY ARG GLY SER MET THR ASN THR LEU SEQRES 4 A 204 GLN VAL LYS LEU LEU SER LYS ASN ALA ARG MET PRO GLU SEQRES 5 A 204 ARG ASN HIS LYS THR ASP ALA GLY TYR ASP ILE PHE SER SEQRES 6 A 204 ALA GLU THR VAL VAL LEU GLU PRO GLN GLU LYS ALA VAL SEQRES 7 A 204 ILE LYS THR ASP VAL ALA VAL SER ILE PRO GLU GLY TYR SEQRES 8 A 204 VAL GLY LEU LEU THR SER ARG SER GLY VAL SER SER LYS SEQRES 9 A 204 THR HIS LEU VAL ILE GLU THR GLY LYS ILE ASP ALA GLY SEQRES 10 A 204 TYR HIS GLY ASN LEU GLY ILE ASN ILE LYS ASN ASP HIS SEQRES 11 A 204 GLU ASP ASP LYS MET GLN THR ILE PHE LEU ARG ASN ILE SEQRES 12 A 204 ASP ASN GLU LYS ILE PHE GLU LYS GLU ARG HIS LEU TYR SEQRES 13 A 204 LYS LEU GLY SER TYR ARG ILE GLU LYS GLY GLU ARG ILE SEQRES 14 A 204 ALA GLN LEU VAL ILE VAL PRO ILE TRP THR PRO GLU LEU SEQRES 15 A 204 LYS GLN VAL GLU GLU PHE GLU SER VAL SER GLU ARG GLY SEQRES 16 A 204 GLU LYS GLY PHE GLY SER SER GLY VAL HET NI A1171 1 HET NI A1172 1 HET DUP A1173 28 HET MG A1174 1 HET PO4 A1175 5 HETNAM NI NICKEL (II) ION HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION FORMUL 2 NI 2(NI 2+) FORMUL 4 DUP C9 H16 N3 O13 P3 FORMUL 5 MG MG 2+ FORMUL 6 PO4 O4 P 3- FORMUL 7 HOH *64(H2 O) HELIX 1 1 ARG A 64 THR A 71 1 8 SHEET 1 AA 2 GLN A 6 LEU A 9 0 SHEET 2 AA 2 VAL A 49 SER A 52 -1 O ALA A 50 N LYS A 8 SHEET 1 AB 4 TYR A 27 PHE A 30 0 SHEET 2 AB 4 ARG A 134 PRO A 142 -1 N ILE A 135 O ILE A 29 SHEET 3 AB 4 TYR A 57 SER A 63 -1 O VAL A 58 N VAL A 141 SHEET 4 AB 4 GLY A 78 ILE A 80 -1 O GLY A 78 N LEU A 61 SHEET 1 AC 2 VAL A 35 LEU A 37 0 SHEET 2 AC 2 TYR A 127 ILE A 129 -1 O TYR A 127 N LEU A 37 SHEET 1 AD 3 LYS A 42 LYS A 46 0 SHEET 2 AD 3 GLY A 89 ASN A 94 -1 O ILE A 90 N ILE A 45 SHEET 3 AD 3 LEU A 73 ILE A 75 -1 O VAL A 74 N LYS A 93 SHEET 1 AE 2 GLN A 102 THR A 103 0 SHEET 2 AE 2 TYR A 122 LYS A 123 -1 O TYR A 122 N THR A 103 SHEET 1 AF 2 LEU A 106 ARG A 107 0 SHEET 2 AF 2 LYS A 113 ILE A 114 -1 O ILE A 114 N LEU A 106 LINK OD1 ASP A 95 NI NI A1171 1555 1555 2.69 LINK OD1 ASP A 95 NI NI A1171 12554 1555 2.69 LINK OD1 ASP A 95 NI NI A1171 6555 1555 2.69 LINK O2G DUP A1173 MG MG A1174 1555 1555 2.86 LINK O2A DUP A1173 MG MG A1174 1555 1555 2.18 LINK O2B DUP A1173 MG MG A1174 1555 1555 2.01 LINK MG MG A1174 O HOH A2062 1555 1555 1.76 SITE 1 AC1 2 ASP A 95 HOH A2014 SITE 1 AC2 1 THR A 77 SITE 1 AC3 22 ARG A 64 SER A 65 GLY A 66 GLY A 78 SITE 2 AC3 22 LYS A 79 ASP A 81 TYR A 84 GLY A 89 SITE 3 AC3 22 GLN A 137 ARG A 160 GLY A 164 PHE A 165 SITE 4 AC3 22 GLY A 166 SER A 167 SER A 168 MG A1174 SITE 5 AC3 22 HOH A2028 HOH A2029 HOH A2032 HOH A2033 SITE 6 AC3 22 HOH A2062 HOH A2063 SITE 1 AC4 2 DUP A1173 HOH A2062 SITE 1 AC5 6 HIS A 72 HIS A 96 ARG A 107 HOH A2013 SITE 2 AC5 6 HOH A2047 HOH A2064 CRYST1 88.657 88.657 88.657 90.00 90.00 90.00 P 21 3 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 0.011279 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011279 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011279 0.00000