HEADER HYDROLASE 13-MAY-03 1PA9 TITLE YERSINIA PROTEIN-TYROSINE PHOSPHATASE COMPLEXED WITH PNCS (YOP51, TITLE 2 PASTEURELLA X,PTPASE,YOP51DELTA162) (CATALYTIC DOMAIN, RESIDUES 163- TITLE 3 468) MUTANT WITH CYS 235 REPLACED BY ARG (C235R) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN-TYROSINE PHOSPHATASE YOPH; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: VIRULENCE PROTEIN; COMPND 6 EC: 3.1.3.48; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA ENTEROCOLITICA; SOURCE 3 ORGANISM_TAXID: 630; SOURCE 4 GENE: YOPH OR YOP51; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PT7-7 KEYWDS HYDROLASE, VIRULENCE EXPDTA X-RAY DIFFRACTION AUTHOR J.P.SUN,L.WU,A.A.FEDOROV,S.C.ALMO,Z.Y.ZHANG REVDAT 6 16-AUG-23 1PA9 1 REMARK REVDAT 5 27-OCT-21 1PA9 1 SEQADV REVDAT 4 29-JUL-20 1PA9 1 AUTHOR JRNL REMARK REVDAT 3 24-FEB-09 1PA9 1 VERSN REVDAT 2 11-NOV-03 1PA9 3 HETATM REVDAT 1 04-NOV-03 1PA9 0 JRNL AUTH J.P.SUN,L.WU,A.A.FEDOROV,S.C.ALMO,Z.Y.ZHANG JRNL TITL CRYSTAL STRUCTURE OF THE YERSINIA PROTEIN-TYROSINE JRNL TITL 2 PHOSPHATASE YOPH COMPLEXED WITH A SPECIFIC SMALL MOLECULE JRNL TITL 3 INHIBITOR JRNL REF J.BIOL.CHEM. V. 278 33392 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12810712 JRNL DOI 10.1074/JBC.M304693200 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 17749 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 688 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2149 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 217 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PA9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAY-03. REMARK 100 THE DEPOSITION ID IS D_1000019202. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAR-02 REMARK 200 TEMPERATURE (KELVIN) : 140 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SDMS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17749 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.31400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1YTW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG1500, IMDAZOLE, PNCS, PH 7.2, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 24.68000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.92000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.92000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.68000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.95000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC 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 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 THR A 23 REMARK 465 SER A 227 REMARK 465 ALA A 228 REMARK 465 VAL A 229 REMARK 465 ALA A 230 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 SER A 226 OG 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 THR A 117 111.81 -38.04 REMARK 500 THR A 156 -133.48 -119.89 REMARK 500 CYS A 241 -114.21 -120.86 REMARK 500 ARG A 242 -60.19 -101.90 REMARK 500 GLN A 264 -3.76 75.95 REMARK 500 ARG A 278 -73.12 -140.84 REMARK 500 VAL A 283 73.11 78.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CSN A 737 DBREF 1PA9 A 23 306 UNP P15273 YOPH_YEREN 185 468 SEQADV 1PA9 ARG A 73 UNP P15273 CYS 235 ENGINEERED MUTATION SEQRES 1 A 284 THR VAL SER PRO TYR GLY PRO GLU ALA ARG ALA GLU LEU SEQRES 2 A 284 SER SER ARG LEU THR THR LEU ARG ASN THR LEU ALA PRO SEQRES 3 A 284 ALA THR ASN ASP PRO ARG TYR LEU GLN ALA CYS GLY GLY SEQRES 4 A 284 GLU LYS LEU ASN ARG PHE ARG ASP ILE GLN CYS ARG ARG SEQRES 5 A 284 GLN THR ALA VAL ARG ALA ASP LEU ASN ALA ASN TYR ILE SEQRES 6 A 284 GLN VAL GLY ASN THR ARG THR ILE ALA CYS GLN TYR PRO SEQRES 7 A 284 LEU GLN SER GLN LEU GLU SER HIS PHE ARG MET LEU ALA SEQRES 8 A 284 GLU ASN ARG THR PRO VAL LEU ALA VAL LEU ALA SER SER SEQRES 9 A 284 SER GLU ILE ALA ASN GLN ARG PHE GLY MET PRO ASP TYR SEQRES 10 A 284 PHE ARG GLN SER GLY THR TYR GLY SER ILE THR VAL GLU SEQRES 11 A 284 SER LYS MET THR GLN GLN VAL GLY LEU GLY ASP GLY ILE SEQRES 12 A 284 MET ALA ASP MET TYR THR LEU THR ILE ARG GLU ALA GLY SEQRES 13 A 284 GLN LYS THR ILE SER VAL PRO VAL VAL HIS VAL GLY ASN SEQRES 14 A 284 TRP PRO ASP GLN THR ALA VAL SER SER GLU VAL THR LYS SEQRES 15 A 284 ALA LEU ALA SER LEU VAL ASP GLN THR ALA GLU THR LYS SEQRES 16 A 284 ARG ASN MET TYR GLU SER LYS GLY SER SER ALA VAL ALA SEQRES 17 A 284 ASP ASP SER LYS LEU ARG PRO VAL ILE HIS CYS ARG ALA SEQRES 18 A 284 GLY VAL GLY ARG THR ALA GLN LEU ILE GLY ALA MET CYS SEQRES 19 A 284 MET ASN ASP SER ARG ASN SER GLN LEU SER VAL GLU ASP SEQRES 20 A 284 MET VAL SER GLN MET ARG VAL GLN ARG ASN GLY ILE MET SEQRES 21 A 284 VAL GLN LYS ASP GLU GLN LEU ASP VAL LEU ILE LYS LEU SEQRES 22 A 284 ALA GLU GLY GLN GLY ARG PRO LEU LEU ASN SER HET CSN A 737 15 HETNAM CSN N,4-DIHYDROXY-N-OXO-3-(SULFOOXY)BENZENAMINIUM FORMUL 2 CSN C6 H5 N O7 S FORMUL 3 HOH *217(H2 O) HELIX 1 1 GLY A 28 ALA A 47 1 20 HELIX 2 2 ARG A 73 ALA A 77 5 5 HELIX 3 3 LEU A 101 SER A 103 5 3 HELIX 4 4 GLN A 104 ASN A 115 1 12 HELIX 5 5 SER A 125 ASN A 131 1 7 HELIX 6 6 GLN A 132 GLY A 135 5 4 HELIX 7 7 SER A 199 LYS A 224 1 26 HELIX 8 8 GLY A 246 ASN A 258 1 13 HELIX 9 9 ASP A 259 SER A 263 5 5 HELIX 10 10 SER A 266 ARG A 278 1 13 HELIX 11 11 LYS A 285 GLN A 299 1 15 SHEET 1 A 8 ALA A 84 VAL A 89 0 SHEET 2 A 8 THR A 92 CYS A 97 -1 O THR A 94 N ILE A 87 SHEET 3 A 8 VAL A 238 HIS A 240 1 O ILE A 239 N ILE A 95 SHEET 4 A 8 LEU A 120 VAL A 122 1 N ALA A 121 O VAL A 238 SHEET 5 A 8 ILE A 182 VAL A 189 1 O VAL A 187 N LEU A 120 SHEET 6 A 8 ILE A 165 GLU A 176 -1 N ILE A 174 O ILE A 182 SHEET 7 A 8 ILE A 149 GLY A 162 -1 N VAL A 159 O ALA A 167 SHEET 8 A 8 GLY A 144 TYR A 146 -1 N GLY A 144 O VAL A 151 SITE 1 AC1 14 PHE A 67 ILE A 70 ASP A 194 GLN A 195 SITE 2 AC1 14 CYS A 241 ARG A 242 ALA A 243 GLY A 244 SITE 3 AC1 14 VAL A 245 GLY A 246 ARG A 247 ILE A 281 SITE 4 AC1 14 GLN A 284 HOH A 810 CRYST1 49.360 55.900 97.840 90.00 90.00 90.00 P 21 21 21 4 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 0.020259 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017889 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010221 0.00000