HEADER ISOMERASE 15-MAR-17 5XB0 TITLE 1.6 A CRYSTAL STRUCTURE OF PEPTIDYL-PROLYL CIS-TRANS ISOMERASE PPIASE TITLE 2 FROM PSEUDOMONAS SYRINGAE PV. TOMATO STR. DC3000 (PSPTO DC3000) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 91-224; COMPND 5 EC: 5.2.1.8; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: [PSEUDOMONAS SYRINGAE] PV. TOMATO STR. DC3000; SOURCE 3 ORGANISM_TAXID: 223283; SOURCE 4 STRAIN: DC3000; SOURCE 5 GENE: PSPTO_0135; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS FKBP, PPIASE, PSPTO-PPIASE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHANG,Y.GAO,M.LI,W.CHANG REVDAT 1 19-APR-17 5XB0 0 SPRSDE 19-APR-17 5XB0 3OE2 JRNL AUTH H.ZHANG,Y.GAO,M.LI,W.CHANG JRNL TITL 1.6 A CRYSTAL STRUCTURE OF PEPTIDYL-PROLYL CIS-TRANS JRNL TITL 2 ISOMERASE PPIASE FROM PSEUDOMONAS SYRINGAE PV. TOMATO STR. JRNL TITL 3 DC3000 (PSPTO DC3000) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 16024 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1600 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 26.5385 - 3.5558 0.99 1466 162 0.1496 0.1833 REMARK 3 2 3.5558 - 2.8233 1.00 1386 154 0.1660 0.1911 REMARK 3 3 2.8233 - 2.4667 1.00 1361 151 0.1912 0.2012 REMARK 3 4 2.4667 - 2.2413 1.00 1354 151 0.1784 0.1993 REMARK 3 5 2.2413 - 2.0808 1.00 1341 148 0.1788 0.2007 REMARK 3 6 2.0808 - 1.9581 1.00 1342 149 0.1620 0.2034 REMARK 3 7 1.9581 - 1.8601 1.00 1346 149 0.1694 0.2041 REMARK 3 8 1.8601 - 1.7791 1.00 1334 148 0.1665 0.2186 REMARK 3 9 1.7791 - 1.7106 1.00 1326 147 0.1717 0.2129 REMARK 3 10 1.7106 - 1.6516 0.91 1210 134 0.1767 0.2265 REMARK 3 11 1.6516 - 1.6000 0.72 958 107 0.2000 0.2549 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.00 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1048 REMARK 3 ANGLE : 1.081 1428 REMARK 3 CHIRALITY : 0.044 159 REMARK 3 PLANARITY : 0.005 190 REMARK 3 DIHEDRAL : 12.411 389 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5XB0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1300003209. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0-7.5 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 FR-E DW 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16027 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 41.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 11.80 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : 0.05200 REMARK 200 FOR THE DATA SET : 49.2400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.26900 REMARK 200 R SYM FOR SHELL (I) : 0.25400 REMARK 200 FOR SHELL : 5.800 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: 1FD9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4M PPOTASSIUM SODIUM TARTRATE, PH REMARK 280 7.3, EVAPORATION, TEMPERATURE 291K 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 16.61100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.15600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.04950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.15600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.61100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.04950 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 TOTAL BURIED SURFACE AREA: 340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 ALA A 197 -112.94 -130.72 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 TLA A 301 DBREF 5XB0 A 92 224 UNP Q88B84 Q88B84_PSESM 92 224 SEQRES 1 A 133 GLY THR ASP ALA PRO THR GLU ALA ALA LEU LYS ALA GLU SEQRES 2 A 133 ARG THR PHE MET ALA GLY GLU LYS ALA LYS PRO GLY VAL SEQRES 3 A 133 LYS GLU LEU ALA ASP GLY ILE LEU MET THR GLU LEU THR SEQRES 4 A 133 PRO GLY THR GLY PRO LYS PRO ASP ALA ASN GLY ARG VAL SEQRES 5 A 133 GLU VAL ARG TYR VAL GLY ARG LEU PRO ASP GLY LYS ILE SEQRES 6 A 133 PHE ASP GLN SER THR GLN PRO GLN TRP PHE ARG LEU ASP SEQRES 7 A 133 SER VAL ILE SER GLY TRP THR SER ALA LEU GLN ASN MET SEQRES 8 A 133 PRO THR GLY ALA LYS TRP ARG LEU VAL ILE PRO SER ASP SEQRES 9 A 133 GLN ALA TYR GLY ALA GLU GLY ALA GLY ASP LEU ILE ASP SEQRES 10 A 133 PRO PHE THR PRO LEU VAL PHE GLU ILE GLU LEU ILE ALA SEQRES 11 A 133 VAL SER GLN HET TLA A 301 10 HETNAM TLA L(+)-TARTARIC ACID FORMUL 2 TLA C4 H6 O6 FORMUL 3 HOH *172(H2 O) HELIX 1 AA1 PRO A 96 ALA A 113 1 18 HELIX 2 AA2 ALA A 121 GLY A 123 5 3 HELIX 3 AA3 ASP A 169 VAL A 171 5 3 HELIX 4 AA4 ILE A 172 LEU A 179 1 8 HELIX 5 AA5 GLN A 180 MET A 182 5 3 HELIX 6 AA6 PRO A 193 ALA A 197 5 5 SHEET 1 AA1 6 LYS A 118 GLU A 119 0 SHEET 2 AA1 6 LEU A 125 THR A 130 -1 O MET A 126 N LYS A 118 SHEET 3 AA1 6 LYS A 187 ILE A 192 -1 O ARG A 189 N THR A 127 SHEET 4 AA1 6 LEU A 213 SER A 223 -1 O PHE A 215 N LEU A 190 SHEET 5 AA1 6 ARG A 142 ARG A 150 -1 N ARG A 150 O VAL A 214 SHEET 6 AA1 6 ILE A 156 GLN A 159 -1 O ASP A 158 N GLY A 149 SHEET 1 AA2 6 LYS A 118 GLU A 119 0 SHEET 2 AA2 6 LEU A 125 THR A 130 -1 O MET A 126 N LYS A 118 SHEET 3 AA2 6 LYS A 187 ILE A 192 -1 O ARG A 189 N THR A 127 SHEET 4 AA2 6 LEU A 213 SER A 223 -1 O PHE A 215 N LEU A 190 SHEET 5 AA2 6 ARG A 142 ARG A 150 -1 N ARG A 150 O VAL A 214 SHEET 6 AA2 6 GLN A 164 ARG A 167 -1 O GLN A 164 N VAL A 145 SITE 1 AC1 5 ASP A 158 VAL A 171 ILE A 172 TRP A 175 SITE 2 AC1 5 TYR A 198 CRYST1 33.222 44.099 82.312 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 0.030101 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022676 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012149 0.00000 MASTER 225 0 1 6 12 0 2 6 0 0 0 11 END