spacer
spacer

PDBsum entry 2ppo

Go to PDB code: 
Top Page protein links
Lyase PDB id
2ppo
Jmol
Contents
Protein chain
107 a.a.
Waters ×137
HEADER    LYASE                                   30-APR-07   2PPO
TITLE     CRYSTAL STRUCTURE OF E60A MUTANT OF FKBP12
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: FK506-BINDING PROTEIN 1A;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE, PPIASE,
COMPND   5 ROTAMASE, 12 KDA FKBP, FKBP-12, IMMUNOPHILIN FKBP12;
COMPND   6 EC: 5.2.1.8;
COMPND   7 ENGINEERED: YES;
COMPND   8 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: FKBP1A, FKBP1, FKBP12;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS    HIGH RESOLUTION PROTEIN STRUCTURE, LYASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    S.SZEP,S.PARK,G.D.VANDUYNE,J.G.SAVEN
REVDAT   3   31-MAR-10 2PPO    1       JRNL
REVDAT   2   24-FEB-09 2PPO    1       VERSN
REVDAT   1   27-MAY-08 2PPO    0
JRNL        AUTH   S.SZEP,S.PARK,E.T.BODER,G.D.VAN DUYNE,J.G.SAVEN
JRNL        TITL   STRUCTURAL COUPLING BETWEEN FKBP12 AND BURIED
JRNL        TITL 2 WATER.
JRNL        REF    PROTEINS                      V.  74   603 2009
JRNL        REFN                   ISSN 0887-3585
JRNL        PMID   18704951
JRNL        DOI    10.1002/PROT.22176
REMARK   2
REMARK   2 RESOLUTION.    1.29 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) : 1.29
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 25.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL
REMARK   3   COMPLETENESS FOR RANGE        (%) : 92.5
REMARK   3   CROSS-VALIDATION METHOD           : THROUGHOUT
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) : 0.189
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 0.189
REMARK   3   FREE R VALUE                  (NO CUTOFF) : 0.182
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : 1471
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 31805
REMARK   3
REMARK   3  FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK   3   R VALUE   (WORKING + TEST SET, F>4SIG(F)) : NULL
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)) : NULL
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS      : 869
REMARK   3   NUCLEIC ACID ATOMS : 0
REMARK   3   HETEROGEN ATOMS    : 0
REMARK   3   SOLVENT ATOMS      : 137
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       : NULL
REMARK   3   NUMBER OF RESTRAINTS                     : NULL
REMARK   3
REMARK   3  RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK   3   BOND LENGTHS                         (A) : 0.007
REMARK   3   ANGLE DISTANCES                      (A) : 1.205
REMARK   3   SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL
REMARK   3   DISTANCES FROM RESTRAINT PLANES      (A) : NULL
REMARK   3   ZERO CHIRAL VOLUMES               (A**3) : NULL
REMARK   3   NON-ZERO CHIRAL VOLUMES           (A**3) : NULL
REMARK   3   ANTI-BUMPING DISTANCE RESTRAINTS     (A) : NULL
REMARK   3   RIGID-BOND ADP COMPONENTS         (A**2) : NULL
REMARK   3   SIMILAR ADP COMPONENTS            (A**2) : NULL
REMARK   3   APPROXIMATELY ISOTROPIC ADPS      (A**2) : NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED: NULL
REMARK   3
REMARK   3  STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER
REMARK   3   SPECIAL CASE: NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS:
REMARK   3  USED ANISOTROPIC B FACTOR
REMARK   3  REFINEMENT IN SHELX
REMARK   4
REMARK   4 2PPO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAY-07.
REMARK 100 THE RCSB ID CODE IS RCSB042646.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 23-NOV-05
REMARK 200  TEMPERATURE           (KELVIN) : 200
REMARK 200  PH                             : 7.0
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : ALS
REMARK 200  BEAMLINE                       : 8.2.2
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.95370
REMARK 200  MONOCHROMATOR                  : SI 111 CHANNEL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 315
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 29420
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.290
REMARK 200  RESOLUTION RANGE LOW       (A) : 25.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 46.200
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 92.5
REMARK 200  DATA REDUNDANCY                : 3.500
REMARK 200  R MERGE                    (I) : 0.09200
REMARK 200  R SYM                      (I) : 0.09200
REMARK 200   FOR THE DATA SET  : 46.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.35
REMARK 200  COMPLETENESS FOR SHELL     (%) : 80.4
REMARK 200  DATA REDUNDANCY IN SHELL       : 2.80
REMARK 200  R MERGE FOR SHELL          (I) : 0.32000
REMARK 200  R SYM FOR SHELL            (I) : 0.32000
REMARK 200   FOR SHELL         : 3.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: CCP4
REMARK 200 STARTING MODEL: NATIVE FKBP STRUCTURE SOLVED IN THIS STUDY
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 45.78
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.9-2.1 M SODIUM MALEONATE, 50 MM
REMARK 280  DMSO, SLOW BUFFER EXCHANGE INTO 2.5 M SODIUM MALEONEATE NO
REMARK 280  DMSO, IN 10 MINUTE STEPS FOR FREEZING, PH 7.0, VAPOR
REMARK 280  DIFFUSION, HANGING DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,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        0.00000
REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000       31.28150
REMARK 290   SMTRY3   2  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 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: 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  18   NE  -  CZ  -  NH1 ANGL. DEV. =  -3.3 DEGREES
REMARK 500    ARG A  40   NE  -  CZ  -  NH1 ANGL. DEV. =  -3.0 DEGREES
REMARK 500    ARG A  40   NE  -  CZ  -  NH2 ANGL. DEV. =   3.1 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    ARG A  13      -32.02   -133.72
REMARK 500    ALA A  81     -113.05   -131.59
REMARK 500    ILE A  90      -52.12   -126.32
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2PPN   RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF FKBP12
REMARK 900 RELATED ID: 2PPP   RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF E60Q MUTANT OF FKBP12
DBREF  2PPO A    1   107  UNP    P62942   FKB1A_HUMAN      2    108
SEQADV 2PPO ALA A   60  UNP  P62942    GLU    61 ENGINEERED
SEQRES   1 A  107  GLY VAL GLN VAL GLU THR ILE SER PRO GLY ASP GLY ARG
SEQRES   2 A  107  THR PHE PRO LYS ARG GLY GLN THR CYS VAL VAL HIS TYR
SEQRES   3 A  107  THR GLY MET LEU GLU ASP GLY LYS LYS PHE ASP SER SER
SEQRES   4 A  107  ARG ASP ARG ASN LYS PRO PHE LYS PHE MET LEU GLY LYS
SEQRES   5 A  107  GLN GLU VAL ILE ARG GLY TRP ALA GLU GLY VAL ALA GLN
SEQRES   6 A  107  MET SER VAL GLY GLN ARG ALA LYS LEU THR ILE SER PRO
SEQRES   7 A  107  ASP TYR ALA TYR GLY ALA THR GLY HIS PRO GLY ILE ILE
SEQRES   8 A  107  PRO PRO HIS ALA THR LEU VAL PHE ASP VAL GLU LEU LEU
SEQRES   9 A  107  LYS LEU GLU
FORMUL   2  HOH   *137(H2 O)
HELIX    1   1 SER A   39  ASN A   43  1                                   5
HELIX    2   2 ILE A   56  GLN A   65  1                                  10
HELIX    3   3 PRO A   78  ALA A   81  5                                   4
SHEET    1   A 5 VAL A   2  SER A   8  0
SHEET    2   A 5 ARG A  71  ILE A  76 -1  O  LYS A  73   N  GLU A   5
SHEET    3   A 5 LEU A  97  GLU A 107 -1  O  LEU A  97   N  ILE A  76
SHEET    4   A 5 THR A  21  LEU A  30 -1  N  THR A  21   O  GLU A 107
SHEET    5   A 5 LYS A  35  SER A  38 -1  O  ASP A  37   N  GLY A  28
SHEET    1   B 5 VAL A   2  SER A   8  0
SHEET    2   B 5 ARG A  71  ILE A  76 -1  O  LYS A  73   N  GLU A   5
SHEET    3   B 5 LEU A  97  GLU A 107 -1  O  LEU A  97   N  ILE A  76
SHEET    4   B 5 THR A  21  LEU A  30 -1  N  THR A  21   O  GLU A 107
SHEET    5   B 5 PHE A  46  MET A  49 -1  O  PHE A  46   N  VAL A  24
CRYST1   28.793   62.563   32.420  90.00 113.70  90.00 P 1 21 1      2
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      0.034731  0.000000  0.015246        0.00000
SCALE2      0.000000  0.015984  0.000000        0.00000
SCALE3      0.000000  0.000000  0.033686        0.00000
      
PROCHECK
Go to PROCHECK summary
 References