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PDBsum entry 1c25

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Hydrolase PDB id
1c25
Jmol
Contents
Protein chain
161 a.a.
Waters ×82
HEADER    HYDROLASE                               17-APR-98   1C25
TITLE     HUMAN CDC25A CATALYTIC DOMAIN
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: CDC25A;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: CATALYTIC DOMAIN;
COMPND   5 SYNONYM: M-PHASE INDUCER PHOSPHATASE 1;
COMPND   6 EC: 3.1.3.48;
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 CELL_LINE: BL21;
SOURCE   6 CELLULAR_LOCATION: CYTOPLASM;
SOURCE   7 GENE: CDC25A;
SOURCE   8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE   9 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE  10 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3);
SOURCE  11 EXPRESSION_SYSTEM_VECTOR: PET21A;
SOURCE  12 EXPRESSION_SYSTEM_PLASMID: BL21
KEYWDS    HYDROLASE, CELL CYCLE PHOSPHATASE,DUAL SPECIFICITY PROTEIN
KEYWDS   2 PHOSPHATASE, CDK2
EXPDTA    X-RAY DIFFRACTION
AUTHOR    E.B.FAUMAN,J.P.COGSWELL,B.LOVEJOY,W.J.ROCQUE,W.HOLMES,
AUTHOR   2 V.G.MONTANA,H.PIWNICA-WORMS,M.J.RINK,M.A.SAPER
REVDAT   2   24-FEB-09 1C25    1       VERSN
REVDAT   1   19-AUG-98 1C25    0
JRNL        AUTH   E.B.FAUMAN,J.P.COGSWELL,B.LOVEJOY,W.J.ROCQUE,
JRNL        AUTH 2 W.HOLMES,V.G.MONTANA,H.PIWNICA-WORMS,M.J.RINK,
JRNL        AUTH 3 M.A.SAPER
JRNL        TITL   CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THE
JRNL        TITL 2 HUMAN CELL CYCLE CONTROL PHOSPHATASE, CDC25A.
JRNL        REF    CELL(CAMBRIDGE,MASS.)         V.  93   617 1998
JRNL        REFN                   ISSN 0092-8674
JRNL        PMID   9604936
JRNL        DOI    10.1016/S0092-8674(00)81190-3
REMARK   1
REMARK   2
REMARK   2 RESOLUTION.    2.30 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : X-PLOR 3.851
REMARK   3   AUTHORS     : BRUNGER
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 99.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : 10000.000
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : 0.0000
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 97.8
REMARK   3   NUMBER OF REFLECTIONS             : 9429
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM
REMARK   3   R VALUE            (WORKING SET) : 0.227
REMARK   3   FREE R VALUE                     : 0.296
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.000
REMARK   3   FREE R VALUE TEST SET COUNT      : 467
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : 0.014
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : 30
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 2.30
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.33
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 99.70
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 290
REMARK   3   BIN R VALUE           (WORKING SET) : 0.3390
REMARK   3   BIN FREE R VALUE                    : 0.4290
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 5.00
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 16
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 0.107
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 1329
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 0
REMARK   3   SOLVENT ATOMS            : 82
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 34.00
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 36.00
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  ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM LUZZATI PLOT        (A) : NULL
REMARK   3   ESD FROM SIGMAA              (A) : NULL
REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL
REMARK   3
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : NULL
REMARK   3   ESD FROM C-V SIGMAA          (A) : NULL
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   BOND LENGTHS                 (A) : 0.013
REMARK   3   BOND ANGLES            (DEGREES) : 1.59
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 24.90
REMARK   3   IMPROPER ANGLES        (DEGREES) : 1.54
REMARK   3
REMARK   3  ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA
REMARK   3   MAIN-CHAIN BOND              (A**2) : 1.000 ; 1.500
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : 1.900 ; 2.000
REMARK   3   SIDE-CHAIN BOND              (A**2) : 1.000 ; 1.500
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : 1.900 ; 2.000
REMARK   3
REMARK   3  NCS MODEL : NULL
REMARK   3
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  PARAMETER FILE  1  : PARHCSDX.PRO
REMARK   3  PARAMETER FILE  2  : PARAM11.WAT
REMARK   3  PARAMETER FILE  3  : NULL
REMARK   3  TOPOLOGY FILE  1   : TOPHCSDX.PRO
REMARK   3  TOPOLOGY FILE  2   : PARAM11.WAT
REMARK   3  TOPOLOGY FILE  3   : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 1C25 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : AUG-97
REMARK 200  TEMPERATURE           (KELVIN) : 120
REMARK 200  PH                             : 5.8-7.4
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : N
REMARK 200  RADIATION SOURCE               : ROTATING ANODE
REMARK 200  BEAMLINE                       : NULL
REMARK 200  X-RAY GENERATOR MODEL          : RIGAKU RUH3R
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.5418
REMARK 200  MONOCHROMATOR                  : NI FILTER
REMARK 200  OPTICS                         : MIRRORS
REMARK 200
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU RAXIS IV
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 12551
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.100
REMARK 200  RESOLUTION RANGE LOW       (A) : NULL
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 98.3
REMARK 200  DATA REDUNDANCY                : 3.000
REMARK 200  R MERGE                    (I) : 0.06700
REMARK 200  R SYM                      (I) : 0.06700
REMARK 200   FOR THE DATA SET  : 18.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.18
REMARK 200  COMPLETENESS FOR SHELL     (%) : 100.0
REMARK 200  DATA REDUNDANCY IN SHELL       : 3.00
REMARK 200  R MERGE FOR SHELL          (I) : 0.37200
REMARK 200  R SYM FOR SHELL            (I) : 0.37200
REMARK 200   FOR SHELL         : 3.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR
REMARK 200 SOFTWARE USED: X-PLOR 3.851
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 40.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 4 MICROLITERS PROTEIN (10 MG/ML IN
REMARK 280  200 MM NACL, 1 MM DTT, 20 MM HEPES, PH 7.4) MIXED WITH 4
REMARK 280  MICROLITERS WELL BUFFER (18-20% PEG 3350, 0.025% BETA-
REMARK 280  OCTYLGLUCOSIDE, 0.11 M SODIUM CITRATE, PH 5.8)
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,-Y,Z+1/2
REMARK 290       3555   -Y,X,Z+1/4
REMARK 290       4555   Y,-X,Z+3/4
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        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       58.54800
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       29.27400
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       87.82200
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 480
REMARK 480 ZERO OCCUPANCY ATOM
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 480   M RES C SSEQI ATOMS
REMARK 480     LYS A  377   CG    CD    CE    NZ
REMARK 480     LYS A  396   CG    CD    CE    NZ
REMARK 480     LYS A  456   CG    CD    CE    NZ
REMARK 480     LYS A  470   CG    CD    CE    NZ
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   907     O    HOH A   917              2.06
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    PRO A 415     -159.82   -110.26
REMARK 500    ILE A 416      -92.10     66.54
REMARK 500    VAL A 417      172.76     57.70
REMARK 500    PRO A 418       91.38    -67.40
REMARK 500    ASP A 420       12.37     35.22
REMARK 500    CYS A 430     -128.56   -134.39
REMARK 500    GLU A 435      -70.96     82.91
REMARK 500    LYS A 494       33.16   -170.48
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  96        DISTANCE =  5.30 ANGSTROMS
REMARK 525    HOH A 905        DISTANCE =  8.64 ANGSTROMS
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: DSU
REMARK 800 EVIDENCE_CODE: UNKNOWN
REMARK 800 SITE_DESCRIPTION: CYS A 384 AND CYS A 340 MAY FORM DISULFIDE
REMARK 800  BOND UNDER CERTAIN CONDITIONS. SEE REFERENCE 1.
REMARK 800 SITE_IDENTIFIER: POP
REMARK 800 EVIDENCE_CODE: UNKNOWN
REMARK 800 SITE_DESCRIPTION: PUTATIVE PHOSPHATE BINDING LOOP, CYS-X(5)-ARG
REMARK 800  SIGNATURE MOTIF.
DBREF  1C25 A  336   495  UNP    P30304   MPIP1_HUMAN    336    495
SEQRES   1 A  161  MET LEU ILE GLY ASP PHE SER LYS GLY TYR LEU PHE HIS
SEQRES   2 A  161  THR VAL ALA GLY LYS HIS GLN ASP LEU LYS TYR ILE SER
SEQRES   3 A  161  PRO GLU ILE MET ALA SER VAL LEU ASN GLY LYS PHE ALA
SEQRES   4 A  161  ASN LEU ILE LYS GLU PHE VAL ILE ILE ASP CYS ARG TYR
SEQRES   5 A  161  PRO TYR GLU TYR GLU GLY GLY HIS ILE LYS GLY ALA VAL
SEQRES   6 A  161  ASN LEU HIS MET GLU GLU GLU VAL GLU ASP PHE LEU LEU
SEQRES   7 A  161  LYS LYS PRO ILE VAL PRO THR ASP GLY LYS ARG VAL ILE
SEQRES   8 A  161  VAL VAL PHE HIS CYS GLU PHE SER SER GLU ARG GLY PRO
SEQRES   9 A  161  ARG MET CYS ARG TYR VAL ARG GLU ARG ASP ARG LEU GLY
SEQRES  10 A  161  ASN GLU TYR PRO LYS LEU HIS TYR PRO GLU LEU TYR VAL
SEQRES  11 A  161  LEU LYS GLY GLY TYR LYS GLU PHE PHE MET LYS CYS GLN
SEQRES  12 A  161  SER TYR CYS GLU PRO PRO SER TYR ARG PRO MET HIS HIS
SEQRES  13 A  161  GLU ASP PHE LYS GLU
FORMUL   2  HOH   *82(H2 O)
HELIX    1   1 PRO A  361  LEU A  368  1                                   8
HELIX    2   2 PRO A  387  GLY A  392  1                                   6
HELIX    3   3 GLU A  404  PHE A  410  1                                   7
HELIX    4   4 ARG A  436  LEU A  450  1                                  15
HELIX    5   5 GLY A  468  LYS A  475  1                                   8
HELIX    6   6 GLN A  477  TYR A  479  5                                   3
SHEET    1   A 3 LEU A 462  VAL A 464  0
SHEET    2   A 3 ARG A 423  HIS A 429  1  N  VAL A 426   O  TYR A 463
SHEET    3   A 3 ILE A 376  ASP A 383  1  N  LYS A 377   O  ARG A 423
SLTBRG       OD1 ASP A 383                 NE  ARG A 385   1555    1555
SLTBRG       OD2 ASP A 383                 NH2 ARG A 385   1555    1555
CISPEP   1 TYR A  454    PRO A  455          0         0.58
CISPEP   2 GLU A  481    PRO A  482          0        -0.70
SITE     1 DSU  2 CYS A 430  CYS A 384
SITE     1 POP  7 CYS A 430  GLU A 431  PHE A 432  SER A 433
SITE     2 POP  7 SER A 434  GLU A 435  ARG A 436
CRYST1   43.507   43.507  117.096  90.00  90.00  90.00 P 41          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      0.022985  0.000000  0.000000        0.00000
SCALE2      0.000000  0.022985  0.000000        0.00000
SCALE3      0.000000  0.000000  0.008540        0.00000
      
PROCHECK
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 References