HEADER ISOMERASE 18-MAR-15 4YUL TITLE MULTICONFORMER SYNCHROTRON MODEL OF CYPA AT 280 K COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PPIASE A,CYCLOPHILIN A,CYCLOSPORIN A-BINDING PROTEIN, COMPND 5 ROTAMASE A; COMPND 6 EC: 5.2.1.8; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PPIA, CYPA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYCLOPHILIN, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.A.KEEDY,L.R.KENNER,M.WARKENTIN,R.A.WOLDEYES,M.C.THOMPSON, AUTHOR 2 A.S.BREWSTER,A.H.VAN BENSCHOTEN,E.L.BAXTER,J.B.HOPKINS, AUTHOR 3 M.UERVIROJNANGKOORN,S.E.MCPHILLIPS,J.SONG,R.A.MORI,J.M.HOLTON, AUTHOR 4 W.I.WEIS,A.T.BRUNGER,M.SOLTIS,H.LEMKE,A.GONZALEZ,N.K.SAUTER, AUTHOR 5 A.E.COHEN,H.VAN DEN BEDEM,R.E.THORNE,J.S.FRASER REVDAT 2 27-SEP-23 4YUL 1 REMARK REVDAT 1 14-OCT-15 4YUL 0 JRNL AUTH D.A.KEEDY,L.R.KENNER,M.WARKENTIN,R.A.WOLDEYES,J.B.HOPKINS, JRNL AUTH 2 M.C.THOMPSON,A.S.BREWSTER,A.H.VAN BENSCHOTEN,E.L.BAXTER, JRNL AUTH 3 M.UERVIROJNANGKOORN,S.E.MCPHILLIPS,J.SONG,R.ALONSO-MORI, JRNL AUTH 4 J.M.HOLTON,W.I.WEIS,A.T.BRUNGER,S.M.SOLTIS,H.LEMKE, JRNL AUTH 5 A.GONZALEZ,N.K.SAUTER,A.E.COHEN,H.VAN DEN BEDEM,R.E.THORNE, JRNL AUTH 6 J.S.FRASER JRNL TITL MAPPING THE CONFORMATIONAL LANDSCAPE OF A DYNAMIC ENZYME BY JRNL TITL 2 MULTITEMPERATURE AND XFEL CRYSTALLOGRAPHY. JRNL REF ELIFE V. 4 2015 JRNL REFN ESSN 2050-084X JRNL PMID 26422513 JRNL DOI 10.7554/ELIFE.07574 REMARK 2 REMARK 2 RESOLUTION. 1.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 38762 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.112 REMARK 3 R VALUE (WORKING SET) : 0.111 REMARK 3 FREE R VALUE : 0.143 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1217 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 25.2329 - 2.9524 0.98 4316 140 0.1059 0.1350 REMARK 3 2 2.9524 - 2.3439 1.00 4231 139 0.1211 0.1510 REMARK 3 3 2.3439 - 2.0478 1.00 4187 135 0.0978 0.1348 REMARK 3 4 2.0478 - 1.8606 1.00 4160 135 0.0911 0.1281 REMARK 3 5 1.8606 - 1.7273 1.00 4157 133 0.0927 0.1094 REMARK 3 6 1.7273 - 1.6255 1.00 4123 135 0.1063 0.1552 REMARK 3 7 1.6255 - 1.5441 1.00 4126 133 0.1257 0.1703 REMARK 3 8 1.5441 - 1.4769 1.00 4122 134 0.1634 0.1846 REMARK 3 9 1.4769 - 1.4200 1.00 4123 133 0.2261 0.2547 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.140 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 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 : 0.008 2018 REMARK 3 ANGLE : 1.162 2784 REMARK 3 CHIRALITY : 0.079 277 REMARK 3 PLANARITY : 0.006 390 REMARK 3 DIHEDRAL : 12.342 768 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 4YUL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207930. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 280 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9767 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38763 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 25.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 1.00000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.520 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: 2CPL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN BY MIXING EQUAL REMARK 280 VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 REMARK 280 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM REMARK 280 NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT., VAPOR DIFFUSION, REMARK 280 HANGING DROP, 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 21.50000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.56000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.30500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.56000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.50000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.30500 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 MET A 1 REMARK 465 GLU A 165 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 NH2 ARG A 148 O HOH A 201 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 OE2 GLU A 134 HZ1 LYS A 155 3545 1.58 REMARK 500 O HOH A 207 O HOH A 341 3555 2.12 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 PHE A 60 -76.17 -139.21 REMARK 500 PHE A 60 -73.36 -139.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YUG RELATED DB: PDB REMARK 900 RELATED ID: 4YUH RELATED DB: PDB REMARK 900 RELATED ID: 4YUI RELATED DB: PDB REMARK 900 RELATED ID: 4YUJ RELATED DB: PDB REMARK 900 RELATED ID: 4YUK RELATED DB: PDB REMARK 900 RELATED ID: 4YUM RELATED DB: PDB REMARK 900 RELATED ID: 4YUN RELATED DB: PDB REMARK 900 RELATED ID: 4YUO RELATED DB: PDB REMARK 900 RELATED ID: 4YUP RELATED DB: PDB DBREF 4YUL A 1 165 UNP P62937 PPIA_HUMAN 1 165 SEQRES 1 A 165 MET VAL ASN PRO THR VAL PHE PHE ASP ILE ALA VAL ASP SEQRES 2 A 165 GLY GLU PRO LEU GLY ARG VAL SER PHE GLU LEU PHE ALA SEQRES 3 A 165 ASP LYS VAL PRO LYS THR ALA GLU ASN PHE ARG ALA LEU SEQRES 4 A 165 SER THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SER CYS SEQRES 5 A 165 PHE HIS ARG ILE ILE PRO GLY PHE MET CYS GLN GLY GLY SEQRES 6 A 165 ASP PHE THR ARG HIS ASN GLY THR GLY GLY LYS SER ILE SEQRES 7 A 165 TYR GLY GLU LYS PHE GLU ASP GLU ASN PHE ILE LEU LYS SEQRES 8 A 165 HIS THR GLY PRO GLY ILE LEU SER MET ALA ASN ALA GLY SEQRES 9 A 165 PRO ASN THR ASN GLY SER GLN PHE PHE ILE CYS THR ALA SEQRES 10 A 165 LYS THR GLU TRP LEU ASP GLY LYS HIS VAL VAL PHE GLY SEQRES 11 A 165 LYS VAL LYS GLU GLY MET ASN ILE VAL GLU ALA MET GLU SEQRES 12 A 165 ARG PHE GLY SER ARG ASN GLY LYS THR SER LYS LYS ILE SEQRES 13 A 165 THR ILE ALA ASP CYS GLY GLN LEU GLU FORMUL 2 HOH *183(H2 O) HELIX 1 AA1 VAL A 29 GLY A 42 1 14 HELIX 2 AA2 THR A 119 ASP A 123 5 5 HELIX 3 AA3 GLY A 135 ARG A 144 1 10 SHEET 1 AA1 9 THR A 5 VAL A 12 0 SHEET 2 AA1 9 GLU A 15 LEU A 24 -1 O GLY A 18 N ILE A 10 SHEET 3 AA1 9 VAL A 128 GLU A 134 -1 O LYS A 133 N SER A 21 SHEET 4 AA1 9 ILE A 97 MET A 100 -1 N LEU A 98 O PHE A 129 SHEET 5 AA1 9 PHE A 112 CYS A 115 -1 O CYS A 115 N ILE A 97 SHEET 6 AA1 9 MET A 61 GLY A 64 -1 N CYS A 62 O ILE A 114 SHEET 7 AA1 9 CYS A 52 ILE A 57 -1 N ARG A 55 O GLN A 63 SHEET 8 AA1 9 ILE A 156 GLN A 163 -1 O ILE A 156 N PHE A 53 SHEET 9 AA1 9 THR A 5 VAL A 12 -1 N ASP A 9 O ASP A 160 CRYST1 43.000 52.610 89.120 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 0.023256 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019008 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011221 0.00000