PDB Short entry for 3BLT HEADER HYDROLASE 11-DEC-07 3BLT TITLE CRYSTAL STRUCTURES OF YOPH COMPLEXED WITH PVSN AND PVS, INHIBITORS OF TITLE 2 YOPH WHICH CO-VALENT BIND TO CYS OF ACTIVE SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN PHOSPHATASE YOPH; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: YOPH CATALYTIC DOMAIN; COMPND 5 SYNONYM: VIRULENCE PROTEIN; COMPND 6 EC: 3.1.3.48; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA ENTEROCOLITICA; SOURCE 3 ORGANISM_TAXID: 630; SOURCE 4 GENE: YOPH, YOP51; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS CO-VALENT BINDING, BINDING AFFINITY, BINDING SELECTIVITY, HYDROLASE, KEYWDS 2 MEMBRANE, OUTER MEMBRANE, PLASMID, PROTEIN PHOSPHATASE, SECRETED, KEYWDS 3 VIRULENCE EXPDTA X-RAY DIFFRACTION AUTHOR S.LIU,Z.-Y.ZHANG REVDAT 3 30-AUG-23 3BLT 1 REMARK SEQADV LINK REVDAT 2 24-JAN-18 3BLT 1 AUTHOR REVDAT 1 10-FEB-09 3BLT 0 JRNL AUTH S.LIU,B.ZHOU,H.YANG,Y.HE,Z.X.JIANG,S.KUMAR,L.WU,Z.Y.ZHANG JRNL TITL ARYL VINYL SULFONATES AND SULFONES AS ACTIVE SITE-DIRECTED JRNL TITL 2 AND MECHANISM-BASED PROBES FOR PROTEIN TYROSINE JRNL TITL 3 PHOSPHATASES. JRNL REF J.AM.CHEM.SOC. V. 130 8251 2008 JRNL REFN ISSN 0002-7863 JRNL PMID 18528979 JRNL DOI 10.1021/JA711125P REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 12279 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 SET) : 0.180 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 2166 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 94 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) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.240 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 3BLT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045676. 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 : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16695 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1PA9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% W/V POLY(ETHYLENE GLYCOL) 3350, REMARK 280 100 MM NACL ,AND 100 MM HEPES BUFFER (PH7.5). , VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 24.61850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.77250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.80450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.77250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.61850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.80450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 ARG A 164 REMARK 465 GLU A 165 REMARK 465 ARG A 166 REMARK 465 PRO A 167 REMARK 465 HIS A 168 REMARK 465 THR A 169 REMARK 465 SER A 170 REMARK 465 GLY A 171 REMARK 465 HIS A 172 REMARK 465 HIS A 173 REMARK 465 GLY A 174 REMARK 465 ALA A 175 REMARK 465 GLY A 176 REMARK 465 GLU A 177 REMARK 465 ALA A 178 REMARK 465 ARG A 179 REMARK 465 ALA A 180 REMARK 465 THR A 181 REMARK 465 ALA A 182 REMARK 465 PRO A 183 REMARK 465 SER A 184 REMARK 465 THR A 185 REMARK 465 VAL A 186 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 279 110.19 -32.60 REMARK 500 THR A 318 -134.85 -126.64 REMARK 500 GLU A 338 118.91 -164.96 REMARK 500 HIS A 402 -171.38 -173.92 REMARK 500 CYS A 403 -113.31 -176.49 REMARK 500 VAL A 407 -0.32 -143.35 REMARK 500 ASN A 424 42.92 -103.88 REMARK 500 GLN A 426 -16.03 76.50 REMARK 500 ARG A 440 -68.20 -143.57 REMARK 500 VAL A 445 71.05 73.07 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 PSY A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BLU RELATED DB: PDB DBREF 3BLT A 164 468 UNP P15273 YOPH_YEREN 164 468 SEQADV 3BLT ARG A 235 UNP P15273 CYS 235 CONFLICT SEQRES 1 A 305 ARG GLU ARG PRO HIS THR SER GLY HIS HIS GLY ALA GLY SEQRES 2 A 305 GLU ALA ARG ALA THR ALA PRO SER THR VAL SER PRO TYR SEQRES 3 A 305 GLY PRO GLU ALA ARG ALA GLU LEU SER SER ARG LEU THR SEQRES 4 A 305 THR LEU ARG ASN THR LEU ALA PRO ALA THR ASN ASP PRO SEQRES 5 A 305 ARG TYR LEU GLN ALA CYS GLY GLY GLU LYS LEU ASN ARG SEQRES 6 A 305 PHE ARG ASP ILE GLN CYS ARG ARG GLN THR ALA VAL ARG SEQRES 7 A 305 ALA ASP LEU ASN ALA ASN TYR ILE GLN VAL GLY ASN THR SEQRES 8 A 305 ARG THR ILE ALA CYS GLN TYR PRO LEU GLN SER GLN LEU SEQRES 9 A 305 GLU SER HIS PHE ARG MET LEU ALA GLU ASN ARG THR PRO SEQRES 10 A 305 VAL LEU ALA VAL LEU ALA SER SER SER GLU ILE ALA ASN SEQRES 11 A 305 GLN ARG PHE GLY MET PRO ASP TYR PHE ARG GLN SER GLY SEQRES 12 A 305 THR TYR GLY SER ILE THR VAL GLU SER LYS MET THR GLN SEQRES 13 A 305 GLN VAL GLY LEU GLY ASP GLY ILE MET ALA ASP MET TYR SEQRES 14 A 305 THR LEU THR ILE ARG GLU ALA GLY GLN LYS THR ILE SER SEQRES 15 A 305 VAL PRO VAL VAL HIS VAL GLY ASN TRP PRO ASP GLN THR SEQRES 16 A 305 ALA VAL SER SER GLU VAL THR LYS ALA LEU ALA SER LEU SEQRES 17 A 305 VAL ASP GLN THR ALA GLU THR LYS ARG ASN MET TYR GLU SEQRES 18 A 305 SER LYS GLY SER SER ALA VAL ALA ASP ASP SER LYS LEU SEQRES 19 A 305 ARG PRO VAL ILE HIS CYS ARG ALA GLY VAL GLY ARG THR SEQRES 20 A 305 ALA GLN LEU ILE GLY ALA MET CYS MET ASN ASP SER ARG SEQRES 21 A 305 ASN SER GLN LEU SER VAL GLU ASP MET VAL SER GLN MET SEQRES 22 A 305 ARG VAL GLN ARG ASN GLY ILE MET VAL GLN LYS ASP GLU SEQRES 23 A 305 GLN LEU ASP VAL LEU ILE LYS LEU ALA GLU GLY GLN GLY SEQRES 24 A 305 ARG PRO LEU LEU ASN SER HET PSY A 501 12 HETNAM PSY PHENYL ETHENESULFONATE FORMUL 2 PSY C8 H8 O3 S FORMUL 3 HOH *94(H2 O) HELIX 1 1 GLY A 190 ALA A 209 1 20 HELIX 2 2 ARG A 235 ALA A 239 5 5 HELIX 3 3 LEU A 263 SER A 265 5 3 HELIX 4 4 GLN A 266 ASN A 277 1 12 HELIX 5 5 SER A 287 ASN A 293 1 7 HELIX 6 6 GLN A 294 GLY A 297 5 4 HELIX 7 7 SER A 361 LYS A 386 1 26 HELIX 8 8 SER A 388 ALA A 392 5 5 HELIX 9 9 GLY A 408 ASN A 420 1 13 HELIX 10 10 ASP A 421 SER A 425 5 5 HELIX 11 11 SER A 428 ARG A 440 1 13 HELIX 12 12 LYS A 447 GLN A 461 1 15 SHEET 1 A 8 ALA A 246 VAL A 251 0 SHEET 2 A 8 THR A 254 CYS A 259 -1 O THR A 256 N ILE A 249 SHEET 3 A 8 VAL A 400 HIS A 402 1 O ILE A 401 N ILE A 257 SHEET 4 A 8 LEU A 282 VAL A 284 1 N ALA A 283 O HIS A 402 SHEET 5 A 8 ILE A 344 VAL A 351 1 O PRO A 347 N LEU A 282 SHEET 6 A 8 ILE A 327 GLU A 338 -1 N LEU A 334 O VAL A 346 SHEET 7 A 8 ILE A 311 GLY A 324 -1 N VAL A 321 O ALA A 329 SHEET 8 A 8 GLY A 306 TYR A 308 -1 N GLY A 306 O VAL A 313 LINK SG CYS A 403 C8 PSY A 501 1555 1555 1.73 SITE 1 AC1 11 ASP A 356 GLN A 357 CYS A 403 ARG A 404 SITE 2 AC1 11 ALA A 405 GLY A 406 GLY A 408 ARG A 409 SITE 3 AC1 11 THR A 410 GLN A 446 HOH A 502 CRYST1 49.237 55.609 97.545 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 0.020310 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017983 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010252 0.00000