PDB Short entry for 3ZF6 HEADER HYDROLASE 10-DEC-12 3ZF6 TITLE PHAGE DUTPASES CONTROL TRANSFER OF VIRULENCE GENES BY A PROTO- TITLE 2 ONCOGENIC G PROTEIN-LIKE MECHANISM. (STAPHYLOCOCCUS BACTERIOPHAGE TITLE 3 80ALPHA DUTPASE D81A D110C S168C 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 TRANSF 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 6 20-DEC-23 3ZF6 1 REMARK LINK REVDAT 5 02-MAY-18 3ZF6 1 REMARK REVDAT 4 17-APR-13 3ZF6 1 REMARK SEQADV SEQRES REVDAT 3 03-APR-13 3ZF6 1 TITLE REMARK REVDAT 2 20-MAR-13 3ZF6 1 JRNL REVDAT 1 30-JAN-13 3ZF6 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. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 6578 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) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.100 REMARK 3 FREE R VALUE TEST SET COUNT : 500 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 493 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3200 REMARK 3 BIN FREE R VALUE SET COUNT : 37 REMARK 3 BIN FREE R VALUE : 0.3720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1313 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 50 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -9.01000 REMARK 3 B22 (A**2) : -9.99000 REMARK 3 B33 (A**2) : 19.00000 REMARK 3 B12 (A**2) : 0.78000 REMARK 3 B13 (A**2) : -6.20000 REMARK 3 B23 (A**2) : -6.42000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.148 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.071 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 : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.896 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1363 ; 0.005 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1844 ; 0.869 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 170 ; 4.632 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 61 ;30.793 ;24.754 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 243 ;13.969 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;12.667 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 209 ; 0.049 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1012 ; 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): 680 ; 1.175 ; 6.355 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 850 ; 2.192 ; 9.522 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 683 ; 0.758 ; 6.419 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 K22 K149 AND V157 REMARK 3 ARE TRACED AS ALA BECAUSE OF LACK OF ELECTRON DENSITY. REMARK 4 REMARK 4 3ZF6 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_1290055060. 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 : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 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 : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7102 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 39.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.900 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 3ZEZ REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2-8% TERT-BUTANOL, 0.1M TRID (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 43.73000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.73000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.73000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.73000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.73000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.73000 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 43.73000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 43.73000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 43.73000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 43.73000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 43.73000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 43.73000 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 43.73000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 43.73000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 43.73000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 43.73000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 43.73000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 43.73000 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: 15810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -96.6 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 0.00000 REMARK 350 BIOMT2 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 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 A1173 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2008 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2039 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 22 CG CD CE NZ REMARK 470 LYS A 46 NZ REMARK 470 LYS A 117 CG CD CE NZ REMARK 470 GLU A 147 CG CD OE1 OE2 REMARK 470 LYS A 149 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU A 76 O HOH A 2030 2.17 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 SG CYS A 110 SG CYS A 168 5555 1.08 REMARK 500 OG SER A 167 O HOH A 2050 5555 1.85 REMARK 500 OD1 ASP A 24 NH2 ARG A 160 5555 1.86 REMARK 500 CB CYS A 110 SG CYS A 168 5555 1.92 REMARK 500 NH1 ARG A 134 O VAL A 170 5555 2.02 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 SER A 167 N - CA - CB ANGL. DEV. = -9.7 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 HIS A 21 140.02 69.77 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 NI A1171 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 95 OD1 REMARK 620 2 ASP A 95 OD1 103.9 REMARK 620 3 ASP A 95 OD1 103.9 103.9 REMARK 620 4 HOH A2011 O 159.7 79.3 94.5 REMARK 620 5 HOH A2011 O 79.3 94.5 159.7 80.5 REMARK 620 6 HOH A2011 O 94.5 159.7 79.3 80.5 80.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1171 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UMP 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: 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). DBREF 3ZF6 A 1 170 UNP A4ZF98 A4ZF98_9CAUD 1 170 SEQADV 3ZF6 MET A -33 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 GLY A -32 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 SER A -31 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 SER A -30 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 HIS A -29 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 HIS A -28 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 HIS A -27 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 HIS A -26 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 HIS A -25 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 HIS A -24 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 SER A -23 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 SER A -22 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 GLY A -21 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 LEU A -20 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 VAL A -19 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 PRO A -18 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 ARG A -17 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 GLY A -16 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 SER A -15 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 HIS A -14 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 MET A -13 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 ALA A -12 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 SER A -11 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 MET A -10 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 THR A -9 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 GLY A -8 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 GLY A -7 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 GLN A -6 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 GLN A -5 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 MET A -4 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 GLY A -3 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 ARG A -2 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 GLY A -1 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 SER A 0 UNP A4ZF98 EXPRESSION TAG SEQADV 3ZF6 ALA A 81 UNP A4ZF98 ASP 81 ENGINEERED MUTATION SEQADV 3ZF6 CYS A 110 UNP A4ZF98 ASP 110 ENGINEERED MUTATION SEQADV 3ZF6 CYS A 168 UNP A4ZF98 SER 168 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 ALA 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 CYS 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 CYS GLY VAL HET NI A1171 1 HET UMP A1172 20 HET NI A1173 1 HETNAM NI NICKEL (II) ION HETNAM UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE HETSYN UMP DUMP FORMUL 2 NI 2(NI 2+) FORMUL 3 UMP C9 H13 N2 O8 P FORMUL 5 HOH *50(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 2.66 LINK OD1 ASP A 95 NI NI A1171 9555 1555 2.66 LINK OD1 ASP A 95 NI NI A1171 5555 1555 2.66 LINK NI NI A1171 O HOH A2011 1555 5555 2.18 LINK NI NI A1171 O HOH A2011 1555 9555 2.18 LINK NI NI A1171 O HOH A2011 1555 1555 2.18 CISPEP 1 LYS A 163 GLY A 164 0 -0.09 SITE 1 AC1 2 ASP A 95 HOH A2011 SITE 1 AC2 18 ARG A 64 SER A 65 GLY A 78 LYS A 79 SITE 2 AC2 18 ALA A 81 TYR A 84 LEU A 88 GLY A 89 SITE 3 AC2 18 GLN A 137 GLY A 164 PHE A 165 HOH A2016 SITE 4 AC2 18 HOH A2018 HOH A2027 HOH A2028 HOH A2035 SITE 5 AC2 18 HOH A2036 HOH A2050 CRYST1 87.460 87.460 87.460 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 0.011434 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011434 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011434 0.00000