HEADER HYDROLASE 10-DEC-12 3ZF5 TITLE PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO- TITLE 2 ONCOGENIC G PROTEIN-LIKE MECHANISM. (STAPHYLOCOCCUS BACTERIOPHAGE TITLE 3 80ALPHA DUTPASE Y84F MUTANT WITH DUPNHPP). COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUTPASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.6.1.23; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: STRUCTURE IN PRESENCE OF DUMP 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, PATHOGENICITY ISLAND, SAPI INDUCTION, GENE TRANSFER, KEYWDS 2 MOONLIGHTING PROTEINS, G-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 3ZF5 1 REMARK REVDAT 4 17-APR-13 3ZF5 1 REMARK SEQADV SEQRES REVDAT 3 03-APR-13 3ZF5 1 TITLE REMARK REVDAT 2 20-MAR-13 3ZF5 1 JRNL REVDAT 1 30-JAN-13 3ZF5 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. 3.20 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 89.5 REMARK 3 NUMBER OF REFLECTIONS : 3391 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) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.200 REMARK 3 FREE R VALUE TEST SET COUNT : 150 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) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 265 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.25 REMARK 3 BIN R VALUE (WORKING SET) : 0.3060 REMARK 3 BIN FREE R VALUE SET COUNT : 16 REMARK 3 BIN FREE R VALUE : 0.4370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1304 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 31 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 13.46000 REMARK 3 B22 (A**2) : -8.92000 REMARK 3 B33 (A**2) : -4.54000 REMARK 3 B12 (A**2) : -0.24000 REMARK 3 B13 (A**2) : -26.90000 REMARK 3 B23 (A**2) : -0.18000 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): 0.126 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.267 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.769 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.878 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.807 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1353 ; 0.004 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1831 ; 0.858 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 168 ; 4.115 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 58 ;28.859 ;24.655 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 242 ;13.211 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;17.058 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 208 ; 0.052 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 988 ; 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 ; 0.329 ; 3.006 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 842 ; 0.624 ; 4.509 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 678 ; 0.111 ; 3.021 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. INITIAL MET IS NOT TRACED. RESIDUES F115, K117, E118 REMARK 3 AND E159 ARE TRACED AS A BECAUSE OF LACK OF ELECTRON DENSITY. REMARK 4 REMARK 4 3ZF5 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_1290055059. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4719 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 14.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.17000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 0.3500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 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: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3ZEZ REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2-8% TERT-BUTANOL, 0.1M TRIS (PH 8.5), REMARK 280 30-50% MPD PR 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 44.12000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.12000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.12000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.12000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.12000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.12000 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 44.12000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 44.12000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 44.12000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 44.12000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 44.12000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 44.12000 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 44.12000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 44.12000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 44.12000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 44.12000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 44.12000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 44.12000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 17610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -121.2 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 44.12000 REMARK 350 BIOMT2 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT3 2 1.000000 0.000000 0.000000 -44.12000 REMARK 350 BIOMT1 3 0.000000 0.000000 1.000000 44.12000 REMARK 350 BIOMT2 3 -1.000000 0.000000 0.000000 44.12000 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 A1172 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2015 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2019 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2020 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 CB 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 130 CD OE1 OE2 REMARK 470 GLU A 147 CG CD OE1 OE2 REMARK 470 GLU A 159 CG CD OE1 OE2 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 GLN A 40 -4.29 71.19 REMARK 500 THR A 77 107.85 -58.64 REMARK 500 ASN A 91 98.80 -68.48 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 MG A1173 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DUP A 777 O2G REMARK 620 2 DUP A 777 O2B 72.1 REMARK 620 3 DUP A 777 O2A 63.9 82.0 REMARK 620 4 HOH A2033 O 77.1 144.1 67.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A1172 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2018 O REMARK 620 2 HOH A2018 O 95.4 REMARK 620 3 HOH A2018 O 95.4 95.4 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUP A 777 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1173 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1171 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1172 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZEZ 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 WITH DUPNHPP). 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: 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 3ZF5 A 1 170 UNP A4ZF98 A4ZF98_9CAUD 1 170 SEQADV 3ZF5 MET A -33 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 GLY A -32 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 SER A -31 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 SER A -30 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 HIS A -29 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 HIS A -28 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 HIS A -27 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 HIS A -26 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 HIS A -25 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 HIS A -24 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 SER A -23 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 SER A -22 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 GLY A -21 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 LEU A -20 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 VAL A -19 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 PRO A -18 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 ARG A -17 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 GLY A -16 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 SER A -15 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 HIS A -14 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 MET A -13 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 ALA A -12 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 SER A -11 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 MET A -10 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 THR A -9 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 GLY A -8 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 GLY A -7 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 GLN A -6 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 GLN A -5 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 MET A -4 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 GLY A -3 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 ARG A -2 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 GLY A -1 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 SER A 0 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF5 PHE A 84 UNP A4ZF98 TYR 84 ENGINEERED MUTATION 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 PHE 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 DUP A 777 28 HET NI A1171 1 HET NI A1172 1 HET MG A1173 1 HETNAM DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE HETNAM NI NICKEL (II) ION HETNAM MG MAGNESIUM ION FORMUL 2 DUP C9 H16 N3 O13 P3 FORMUL 3 NI 2(NI 2+) FORMUL 5 MG MG 2+ FORMUL 6 HOH *31(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 LINK O2G DUP A 777 MG MG A1173 1555 1555 2.64 LINK O2B DUP A 777 MG MG A1173 1555 1555 2.11 LINK O2A DUP A 777 MG MG A1173 1555 1555 2.58 LINK NI NI A1172 O HOH A2018 1555 6555 2.00 LINK NI NI A1172 O HOH A2018 1555 12554 2.00 LINK NI NI A1172 O HOH A2018 1555 1555 2.00 LINK MG MG A1173 O HOH A2033 1555 1555 2.15 SITE 1 AC1 22 ASN A 20 ARG A 64 SER A 65 GLY A 66 SITE 2 AC1 22 GLY A 78 LYS A 79 ILE A 80 ASP A 81 SITE 3 AC1 22 PHE A 84 LEU A 88 GLY A 89 GLN A 137 SITE 4 AC1 22 ARG A 160 GLY A 164 PHE A 165 GLY A 166 SITE 5 AC1 22 SER A 167 SER A 168 MG A1173 HOH A2009 SITE 6 AC1 22 HOH A2017 HOH A2033 SITE 1 AC2 4 ASP A 28 ARG A 64 DUP A 777 HOH A2033 SITE 1 AC3 3 HIS A 72 HIS A 96 ARG A 107 SITE 1 AC4 2 ASP A 95 HOH A2018 CRYST1 88.240 88.240 88.240 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 0.011333 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011333 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011333 0.00000