HEADER ISOMERASE 13-JUL-16 5KV5 TITLE HUMAN CYCLOPHILIN A AT 278K, DATA SET 7 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 CONFORMATIONAL VARIATION, RADIATION DAMAGE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.RUSSI,A.GONZALEZ,L.R.KENNER,D.A.KEEDY,J.S.FRASER,H.VAN DEN BEDEM REVDAT 5 04-OCT-23 5KV5 1 REMARK REVDAT 4 27-NOV-19 5KV5 1 REMARK REVDAT 3 27-SEP-17 5KV5 1 REMARK REVDAT 2 11-JAN-17 5KV5 1 JRNL REVDAT 1 10-AUG-16 5KV5 0 JRNL AUTH S.RUSSI,A.GONZALEZ,L.R.KENNER,D.A.KEEDY,J.S.FRASER, JRNL AUTH 2 H.VAN DEN BEDEM JRNL TITL CONFORMATIONAL VARIATION OF PROTEINS AT ROOM TEMPERATURE IS JRNL TITL 2 NOT DOMINATED BY RADIATION DAMAGE. JRNL REF J SYNCHROTRON RADIAT V. 24 73 2017 JRNL REFN ESSN 1600-5775 JRNL PMID 28009548 JRNL DOI 10.1107/S1600577516017343 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.4 REMARK 3 NUMBER OF REFLECTIONS : 20245 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1021 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 3.2512 - 2.5809 0.92 2880 150 0.1636 0.1934 REMARK 3 2 2.5809 - 2.2547 0.91 2830 144 0.1638 0.2231 REMARK 3 3 2.2547 - 2.0486 0.90 2764 158 0.1669 0.2410 REMARK 3 4 2.0486 - 1.9018 0.88 2681 144 0.2016 0.2342 REMARK 3 5 1.9018 - 1.7896 0.85 2605 143 0.2324 0.2870 REMARK 3 6 1.7896 - 1.7000 0.81 2466 134 0.2767 0.3146 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.06 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 1967 REMARK 3 ANGLE : 0.820 2703 REMARK 3 CHIRALITY : 0.059 281 REMARK 3 PLANARITY : 0.005 371 REMARK 3 DIHEDRAL : 12.613 1199 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 5KV5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1000222790. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 278 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.100 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.1.26 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28483 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 38.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.5 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.18800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 2.48400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: NULL REMARK 200 STARTING MODEL: 5F66 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 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 21.48100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.62300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.30600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.62300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.48100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.30600 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 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 O HOH A 207 O HOH A 317 2.13 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 -73.65 -139.55 REMARK 500 PHE A 60 -73.08 -139.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KUL RELATED DB: PDB REMARK 900 RELATED ID: 5KUN RELATED DB: PDB REMARK 900 RELATED ID: 5KUO RELATED DB: PDB REMARK 900 RELATED ID: 5KUQ RELATED DB: PDB REMARK 900 RELATED ID: 5KUR RELATED DB: PDB REMARK 900 RELATED ID: 5KUS RELATED DB: PDB REMARK 900 RELATED ID: 5KUU RELATED DB: PDB REMARK 900 RELATED ID: 5KUV RELATED DB: PDB REMARK 900 RELATED ID: 5KUW RELATED DB: PDB REMARK 900 RELATED ID: 5KUZ RELATED DB: PDB REMARK 900 RELATED ID: 5KV0 RELATED DB: PDB REMARK 900 RELATED ID: 5KV1 RELATED DB: PDB REMARK 900 RELATED ID: 5KV2 RELATED DB: PDB REMARK 900 RELATED ID: 5KV3 RELATED DB: PDB REMARK 900 RELATED ID: 5KV4 RELATED DB: PDB REMARK 900 RELATED ID: 5KV6 RELATED DB: PDB REMARK 900 RELATED ID: 5KV7 RELATED DB: PDB DBREF 5KV5 A 2 165 UNP P62937 PPIA_HUMAN 2 165 SEQRES 1 A 164 VAL ASN PRO THR VAL PHE PHE ASP ILE ALA VAL ASP GLY SEQRES 2 A 164 GLU PRO LEU GLY ARG VAL SER PHE GLU LEU PHE ALA ASP SEQRES 3 A 164 LYS VAL PRO LYS THR ALA GLU ASN PHE ARG ALA LEU SER SEQRES 4 A 164 THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SER CYS PHE SEQRES 5 A 164 HIS ARG ILE ILE PRO GLY PHE MET CYS GLN GLY GLY ASP SEQRES 6 A 164 PHE THR ARG HIS ASN GLY THR GLY GLY LYS SER ILE TYR SEQRES 7 A 164 GLY GLU LYS PHE GLU ASP GLU ASN PHE ILE LEU LYS HIS SEQRES 8 A 164 THR GLY PRO GLY ILE LEU SER MET ALA ASN ALA GLY PRO SEQRES 9 A 164 ASN THR ASN GLY SER GLN PHE PHE ILE CYS THR ALA LYS SEQRES 10 A 164 THR GLU TRP LEU ASP GLY LYS HIS VAL VAL PHE GLY LYS SEQRES 11 A 164 VAL LYS GLU GLY MET ASN ILE VAL GLU ALA MET GLU ARG SEQRES 12 A 164 PHE GLY SER ARG ASN GLY LYS THR SER LYS LYS ILE THR SEQRES 13 A 164 ILE ALA ASP CYS GLY GLN LEU GLU FORMUL 2 HOH *127(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 GLU A 15 N VAL A 12 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 GLY A 130 SHEET 5 AA1 9 PHE A 112 CYS A 115 -1 O PHE A 113 N SER A 99 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 GLU A 165 -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 42.962 52.612 89.246 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 0.023276 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019007 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011205 0.00000