spacer
spacer

PDBsum entry 3o5p

Go to PDB code: 
Top Page protein links
Isomerase PDB id
3o5p
Jmol
Contents
Protein chain
128 a.a.
Waters ×304
HEADER    ISOMERASE                               28-JUL-10   3O5P
TITLE     FK1 DOMAIN MUTANT A19T OF FKBP51, CRYSTAL FORM IV
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FKBP5;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: PPIASE FKBP5, FK506-BINDING PROTEIN 5, FKBP-5, ROTAMASE, 51
COMPND   5 KDA FK506-BINDING PROTEIN, 51 KDA FKBP, FKBP-51, 54 KDA PROGESTERONE
COMPND   6 RECEPTOR-ASSOCIATED IMMUNOPHILIN, FKBP54, P54, FF1 ANTIGEN, HSP90-
COMPND   7 BINDING IMMUNOPHILIN, ANDROGEN-REGULATED PROTEIN 6;
COMPND   8 EC: 5.2.1.8;
COMPND   9 ENGINEERED: YES;
COMPND  10 MUTATION: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   3 ORGANISM_COMMON: HUMAN;
SOURCE   4 ORGANISM_TAXID: 9606;
SOURCE   5 GENE: AIG6, FKBP5, FKBP51;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON+ RIL;
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE  10 EXPRESSION_SYSTEM_PLASMID: PPROEX-HTB
KEYWDS    FK-506 BINDING DOMAIN, HSP90 COCHAPERONE, IMMUNOPHILINE, PEPTIDYL-
KEYWDS   2 PROLYL ISOMERASE, ISOMERASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    A.BRACHER,C.KOZANY,A.-K.THOST,F.HAUSCH
REVDAT   2   28-MAR-12 3O5P    1       JRNL   VERSN
REVDAT   1   01-JUN-11 3O5P    0
JRNL        AUTH   A.BRACHER,C.KOZANY,A.K.THOST,F.HAUSCH
JRNL        TITL   STRUCTURAL CHARACTERIZATION OF THE PPIASE DOMAIN OF FKBP51,
JRNL        TITL 2 A COCHAPERONE OF HUMAN HSP90.
JRNL        REF    ACTA CRYSTALLOGR.,SECT.D      V.  67   549 2011
JRNL        REFN                   ISSN 0907-4449
JRNL        PMID   21636895
JRNL        DOI    10.1107/S0907444911013862
REMARK   2
REMARK   2 RESOLUTION.    1.00 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : SHELXL-97
REMARK   3   AUTHORS     : G.M.SHELDRICK
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.00
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   COMPLETENESS FOR RANGE        (%) : 82.9
REMARK   3   CROSS-VALIDATION METHOD           : FREE R
REMARK   3   FREE R VALUE TEST SET SELECTION   : RANDOM
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : 0.112
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 0.116
REMARK   3   FREE R VALUE                  (NO CUTOFF) : 0.147
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : 3122
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 58981
REMARK   3
REMARK   3  FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK   3   R VALUE   (WORKING + TEST SET, F>4SIG(F)) : 0.109
REMARK   3   R VALUE          (WORKING SET, F>4SIG(F)) : NULL
REMARK   3   FREE R VALUE                  (F>4SIG(F)) : NULL
REMARK   3   FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT   (F>4SIG(F)) : NULL
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (F>4SIG(F)) : 55618
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS      : 982
REMARK   3   NUCLEIC ACID ATOMS : 0
REMARK   3   HETEROGEN ATOMS    : 0
REMARK   3   SOLVENT ATOMS      : 279
REMARK   3
REMARK   3  MODEL REFINEMENT.
REMARK   3   OCCUPANCY SUM OF NON-HYDROGEN ATOMS      : NULL
REMARK   3   OCCUPANCY SUM OF HYDROGEN ATOMS          : NULL
REMARK   3   NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL
REMARK   3   NUMBER OF LEAST-SQUARES PARAMETERS       : 13044
REMARK   3   NUMBER OF RESTRAINTS                     : 17934
REMARK   3
REMARK   3  RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK   3   BOND LENGTHS                         (A) : 0.014
REMARK   3   ANGLE DISTANCES                      (A) : 0.030
REMARK   3   SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000
REMARK   3   DISTANCES FROM RESTRAINT PLANES      (A) : 0.035
REMARK   3   ZERO CHIRAL VOLUMES               (A**3) : 0.083
REMARK   3   NON-ZERO CHIRAL VOLUMES           (A**3) : 0.102
REMARK   3   ANTI-BUMPING DISTANCE RESTRAINTS     (A) : 0.026
REMARK   3   RIGID-BOND ADP COMPONENTS         (A**2) : 0.005
REMARK   3   SIMILAR ADP COMPONENTS            (A**2) : 0.047
REMARK   3   APPROXIMATELY ISOTROPIC ADPS      (A**2) : 0.085
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
REMARK   3
REMARK   3  STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER
REMARK   3   SPECIAL CASE: NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 3O5P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-10.
REMARK 100 THE RCSB ID CODE IS RCSB060697.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 18-DEC-06
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               : SLS
REMARK 200  BEAMLINE                       : X10SA
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.972
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : MARRESEARCH
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200  DATA SCALING SOFTWARE          : SCALA
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 65715
REMARK 200  RESOLUTION RANGE HIGH      (A) : 0.950
REMARK 200  RESOLUTION RANGE LOW       (A) : 39.200
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 79.6
REMARK 200  DATA REDUNDANCY                : 4.200
REMARK 200  R MERGE                    (I) : 0.04400
REMARK 200  R SYM                      (I) : 0.04400
REMARK 200   FOR THE DATA SET  : 21.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.95
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.00
REMARK 200  COMPLETENESS FOR SHELL     (%) : 31.4
REMARK 200  DATA REDUNDANCY IN SHELL       : 2.30
REMARK 200  R MERGE FOR SHELL          (I) : 0.27300
REMARK 200  R SYM FOR SHELL            (I) : 0.27300
REMARK 200   FOR SHELL         : 2.700
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 3O5P
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 46.95
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 25 % PEG3350, 0.2 M NH4OAC, 0.1 M
REMARK 280  HEPES, PH 7.5, VAPOR DIFFUSION, TEMPERATURE 293K
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       21.14450
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       28.32350
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       27.15100
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       28.32350
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       21.14450
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       27.15100
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 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     GLU A 140    CG   CD   OE1  OE2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3
REMARK 500    ARG A  31   NE  -  CZ  -  NH1 ANGL. DEV. =   4.6 DEGREES
REMARK 500    LYS A  65   CD  -  CE  -  NZ  ANGL. DEV. =  14.9 DEGREES
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    ALA A 112     -117.57   -135.61
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525  M RES CSSEQI
REMARK 525    HOH A 216        DISTANCE =  6.31 ANGSTROMS
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3O5D   RELATED DB: PDB
REMARK 900 RELATED ID: 3O5E   RELATED DB: PDB
REMARK 900 RELATED ID: 3O5F   RELATED DB: PDB
REMARK 900 RELATED ID: 3O5G   RELATED DB: PDB
REMARK 900 RELATED ID: 3O5I   RELATED DB: PDB
REMARK 900 RELATED ID: 3O5J   RELATED DB: PDB
REMARK 900 RELATED ID: 3O5K   RELATED DB: PDB
REMARK 900 RELATED ID: 3O5L   RELATED DB: PDB
REMARK 900 RELATED ID: 3O5M   RELATED DB: PDB
REMARK 900 RELATED ID: 3O5O   RELATED DB: PDB
REMARK 900 RELATED ID: 3O5Q   RELATED DB: PDB
REMARK 900 RELATED ID: 3O5R   RELATED DB: PDB
REMARK 900 RELATED ID: 1KT0   RELATED DB: PDB
REMARK 900 STRUCTURE OF FULL-LENGTH FKBP51
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 AUTHORS STATE THAT A19T IS A MUTATION, BUT NOT A NATURALLY
REMARK 999 OCCURRING ALLELE.
DBREF  3O5P A   16   140  UNP    Q13451   FKBP5_HUMAN     16    140
SEQADV 3O5P GLY A   13  UNP  Q13451              EXPRESSION TAG
SEQADV 3O5P ALA A   14  UNP  Q13451              EXPRESSION TAG
SEQADV 3O5P PRO A   15  UNP  Q13451              EXPRESSION TAG
SEQADV 3O5P THR A   19  UNP  Q13451    ALA    19 SEE REMARK 999
SEQRES   1 A  128  GLY ALA PRO ALA THR VAL THR GLU GLN GLY GLU ASP ILE
SEQRES   2 A  128  THR SER LYS LYS ASP ARG GLY VAL LEU LYS ILE VAL LYS
SEQRES   3 A  128  ARG VAL GLY ASN GLY GLU GLU THR PRO MET ILE GLY ASP
SEQRES   4 A  128  LYS VAL TYR VAL HIS TYR LYS GLY LYS LEU SER ASN GLY
SEQRES   5 A  128  LYS LYS PHE ASP SER SER HIS ASP ARG ASN GLU PRO PHE
SEQRES   6 A  128  VAL PHE SER LEU GLY LYS GLY GLN VAL ILE LYS ALA TRP
SEQRES   7 A  128  ASP ILE GLY VAL ALA THR MET LYS LYS GLY GLU ILE CYS
SEQRES   8 A  128  HIS LEU LEU CYS LYS PRO GLU TYR ALA TYR GLY SER ALA
SEQRES   9 A  128  GLY SER LEU PRO LYS ILE PRO SER ASN ALA THR LEU PHE
SEQRES  10 A  128  PHE GLU ILE GLU LEU LEU ASP PHE LYS GLY GLU
FORMUL   2  HOH   *279(H2 O)
HELIX    1   1 GLY A   13  GLY A   22  1                                  10
HELIX    2   2 HIS A   71  ASN A   74  5                                   4
HELIX    3   3 ILE A   87  ALA A   95  1                                   9
HELIX    4   4 PRO A  109  ALA A  112  5                                   4
SHEET    1   A 6 GLU A  23  ASP A  24  0
SHEET    2   A 6 VAL A  33  ARG A  39 -1  O  LYS A  35   N  GLU A  23
SHEET    3   A 6 ILE A 102  CYS A 107 -1  O  HIS A 104   N  ILE A  36
SHEET    4   A 6 LEU A 128  LYS A 138 -1  O  LEU A 128   N  CYS A 107
SHEET    5   A 6 LYS A  52  LEU A  61 -1  N  HIS A  56   O  GLU A 133
SHEET    6   A 6 LYS A  66  SER A  69 -1  O  PHE A  67   N  GLY A  59
SHEET    1   B 6 GLU A  23  ASP A  24  0
SHEET    2   B 6 VAL A  33  ARG A  39 -1  O  LYS A  35   N  GLU A  23
SHEET    3   B 6 ILE A 102  CYS A 107 -1  O  HIS A 104   N  ILE A  36
SHEET    4   B 6 LEU A 128  LYS A 138 -1  O  LEU A 128   N  CYS A 107
SHEET    5   B 6 LYS A  52  LEU A  61 -1  N  HIS A  56   O  GLU A 133
SHEET    6   B 6 PHE A  77  SER A  80 -1  O  PHE A  79   N  VAL A  53
CISPEP   1 LEU A  119    PRO A  120          0         7.22
CRYST1   42.289   54.302   56.647  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      0.023647  0.000000  0.000000        0.00000
SCALE2      0.000000  0.018416  0.000000        0.00000
SCALE3      0.000000  0.000000  0.017653        0.00000
      
PROCHECK
Go to PROCHECK summary
 References