HEADER ISOMERASE 13-JUL-16 5KUO
TITLE HUMAN CYCLOPHILIN A AT 100K, DATA SET 3
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 5KUO 1 REMARK
REVDAT 4 27-SEP-17 5KUO 1 REMARK
REVDAT 3 11-JAN-17 5KUO 1 JRNL
REVDAT 2 14-SEP-16 5KUO 1 ATOM
REVDAT 1 31-AUG-16 5KUO 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) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3
REMARK 3 NUMBER OF REFLECTIONS : 21779
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.177
REMARK 3 R VALUE (WORKING SET) : 0.175
REMARK 3 FREE R VALUE : 0.214
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140
REMARK 3 FREE R VALUE TEST SET COUNT : 1119
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 3.3991 - 2.6983 0.98 2644 139 0.1753 0.2076
REMARK 3 2 2.6983 - 2.3573 0.97 2584 143 0.1890 0.2185
REMARK 3 3 2.3573 - 2.1418 0.97 2579 150 0.1678 0.2250
REMARK 3 4 2.1418 - 1.9883 0.96 2549 130 0.1703 0.2239
REMARK 3 5 1.9883 - 1.8711 0.96 2549 138 0.1824 0.2414
REMARK 3 6 1.8711 - 1.7774 0.96 2500 154 0.1750 0.2363
REMARK 3 7 1.7774 - 1.7000 0.96 2523 131 0.1874 0.2536
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) : 0.170
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.130
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 14.86
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.53
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 1869
REMARK 3 ANGLE : 0.772 2570
REMARK 3 CHIRALITY : 0.060 269
REMARK 3 PLANARITY : 0.005 349
REMARK 3 DIHEDRAL : 11.368 1135
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 5KUO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-16.
REMARK 100 THE DEPOSITION ID IS D_1000222775.
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) : 100
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 : 31586
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480
REMARK 200 RESOLUTION RANGE LOW (A) : 38.260
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4
REMARK 200 DATA REDUNDANCY : 2.800
REMARK 200 R MERGE (I) : 0.05400
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.3000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50
REMARK 200 COMPLETENESS FOR SHELL (%) : 49.3
REMARK 200 DATA REDUNDANCY IN SHELL : 2.20
REMARK 200 R MERGE FOR SHELL (I) : 0.63800
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: 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 (%): 55.69
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78
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 21.17450
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.63550
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.29250
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.63550
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.17450
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.29250
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 THR A 68
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 VAL A 2 CG1 CG2
REMARK 470 GLU A 165 CG CD OE1 OE2
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 248 O HOH A 274 2.02
REMARK 500 O HOH A 202 O HOH A 401 2.08
REMARK 500 O HOH A 277 O HOH A 380 2.08
REMARK 500 O HOH A 328 O HOH A 427 2.17
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 -77.89 -124.14
REMARK 500 ASN A 102 -168.89 -164.49
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI ANGLE
REMARK 500 LYS A 28 12.19
REMARK 500 LYS A 28 12.12
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: 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: 5KV5 RELATED DB: PDB
REMARK 900 RELATED ID: 5KV6 RELATED DB: PDB
REMARK 900 RELATED ID: 5KV7 RELATED DB: PDB
DBREF 5KUO 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 *256(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 8 PHE A 53 ILE A 57 0
SHEET 2 AA1 8 MET A 61 GLY A 64 -1 O GLN A 63 N ARG A 55
SHEET 3 AA1 8 PHE A 112 CYS A 115 -1 O ILE A 114 N CYS A 62
SHEET 4 AA1 8 ILE A 97 MET A 100 -1 N SER A 99 O PHE A 113
SHEET 5 AA1 8 VAL A 128 GLU A 134 -1 O GLY A 130 N LEU A 98
SHEET 6 AA1 8 GLU A 15 LEU A 24 -1 N SER A 21 O LYS A 133
SHEET 7 AA1 8 THR A 5 VAL A 12 -1 N ILE A 10 O GLY A 18
SHEET 8 AA1 8 ILE A 156 LEU A 164 -1 O ASP A 160 N ASP A 9
CRYST1 42.349 52.585 89.271 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 0.023613 0.000000 0.000000 0.00000
SCALE2 0.000000 0.019017 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011202 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
