PDB Short entry for 2PV1 HEADER ISOMERASE 09-MAY-07 2PV1 TITLE CRYSTALLOGRAPHIC STRUCTURE OF SURA FIRST PEPTIDYL-PROLYL ISOMERASE TITLE 2 DOMAIN COMPLEXED WITH PEPTIDE WEYIPNV COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHAPERONE SURA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PPIC 1; COMPND 5 SYNONYM: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE SURA, PPIASE SURA, COMPND 6 ROTAMASE SURA, SURVIVAL PROTEIN A; COMPND 7 EC: 5.2.1.8; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: GLYCOSYL TRANSFERASE, GROUP 1; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: K-12 EMG2; SOURCE 5 GENE: SURA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTYB1; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS SURVIVAL PROTEIN A, PEPTIDYL-PROLYL CIS-TRANS ISOMERASE DOMAIN, KEYWDS 2 COMPLEX, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR X.XU,D.B.MCKAY REVDAT 5 30-AUG-23 2PV1 1 REMARK REVDAT 4 18-OCT-17 2PV1 1 REMARK REVDAT 3 24-FEB-09 2PV1 1 VERSN REVDAT 2 30-OCT-07 2PV1 1 JRNL REVDAT 1 02-OCT-07 2PV1 0 JRNL AUTH X.XU,S.WANG,Y.X.HU,D.B.MCKAY JRNL TITL THE PERIPLASMIC BACTERIAL MOLECULAR CHAPERONE SURA ADAPTS JRNL TITL 2 ITS STRUCTURE TO BIND PEPTIDES IN DIFFERENT CONFORMATIONS TO JRNL TITL 3 ASSERT A SEQUENCE PREFERENCE FOR AROMATIC RESIDUES. JRNL REF J.MOL.BIOL. V. 373 367 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17825319 JRNL DOI 10.1016/J.JMB.2007.07.069 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.BITTO,D.B.MCKAY REMARK 1 TITL CRYSTALLOGRAPHIC STRUCTURE OF SURA, A MOLECULAR CHAPERONE REMARK 1 TITL 2 THAT FACILITATES FOLDING OF OUTER MEMBRANE PORINS REMARK 1 REF STRUCTURE V. 10 1489 2002 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 12429090 REMARK 1 DOI 10.1016/S0969-2126(02)00877-8 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.05 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) (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 25854 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) : 0.226 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 2552 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.38 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE : 0.2930 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 419 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 839 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 132 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.55400 REMARK 3 B22 (A**2) : -0.67000 REMARK 3 B33 (A**2) : 1.22500 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.08 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.060 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 : 44.38 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 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2PV1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000042803. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26586 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.290 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 (%) : 98.4 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 39.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.12600 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1M5Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25~28% POLYETHYLENE GLYCOL REMARK 280 MONOMETHYLETHER 5000, 0.2 M AMMONIUM SULFATE, 0.1 M MES BUFFER, REMARK 280 PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y+1/2,-Z REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 25.94300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.41000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 25.94300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.41000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 25.94300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.41000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 25.94300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.41000 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 DBREF 2PV1 A 172 274 UNP P0ABZ6 SURA_ECOLI 172 274 DBREF 2PV1 B 1 5 UNP Q2RHX9 Q2RHX9_MOOTA 171 175 SEQRES 1 A 103 THR GLU LEU ASN LEU SER HIS ILE LEU ILE PRO LEU PRO SEQRES 2 A 103 GLU ASN PRO THR SER ASP GLN VAL ASN GLU ALA GLU SER SEQRES 3 A 103 GLN ALA ARG ALA ILE VAL ASP GLN ALA ARG ASN GLY ALA SEQRES 4 A 103 ASP PHE GLY LYS LEU ALA ILE ALA HIS SER ALA ASP GLN SEQRES 5 A 103 GLN ALA LEU ASN GLY GLY GLN MET GLY TRP GLY ARG ILE SEQRES 6 A 103 GLN GLU LEU PRO GLY ILE PHE ALA GLN ALA LEU SER THR SEQRES 7 A 103 ALA LYS LYS GLY ASP ILE VAL GLY PRO ILE ARG SER GLY SEQRES 8 A 103 VAL GLY PHE HIS ILE LEU LYS VAL ASN ASP LEU ARG SEQRES 1 B 7 TRP GLU TYR ILE PRO ASN VAL FORMUL 3 HOH *132(H2 O) HELIX 1 1 THR A 188 ASN A 208 1 21 HELIX 2 2 ASP A 211 SER A 220 1 10 HELIX 3 3 GLN A 224 GLY A 228 5 5 HELIX 4 4 ARG A 235 LEU A 239 5 5 HELIX 5 5 PRO A 240 LEU A 247 1 8 SHEET 1 A 4 GLN A 230 GLY A 234 0 SHEET 2 A 4 GLU A 173 PRO A 182 -1 N LEU A 176 O MET A 231 SHEET 3 A 4 GLY A 264 ARG A 274 -1 O ASP A 272 N ASN A 175 SHEET 4 A 4 ILE A 255 SER A 261 -1 N VAL A 256 O LEU A 268 CISPEP 1 GLY A 257 PRO A 258 0 0.29 CRYST1 51.886 98.820 41.053 90.00 90.00 90.00 C 2 2 2 8 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 0.019273 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010119 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024359 0.00000