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PDBsum entry 1yml

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Hydrolase, cell cycle PDB id
1yml
Jmol
Contents
Protein chain
171 a.a.
Metals
_CL
Waters ×172
HEADER    HYDROLASE, CELL CYCLE                   21-JAN-05   1YML
TITLE     CRYSTAL STRUCTURE OF THE CDC25B PHOSPHATASE CATALYTIC
TITLE    2 DOMAIN WITH THE ACTIVE SITE CYSTEINE IN THE SULFENIC FORM
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: M-PHASE INDUCER PHOSPHATASE 2;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: CATALYTIC DOMAIN;
COMPND   5 SYNONYM: CDC25B PHOSPHATASE; DUAL SPECIFICITY PHOSPHATASE
COMPND   6 CDC25B;
COMPND   7 EC: 3.1.3.48;
COMPND   8 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: CDC25B, CDC25HU2;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS    SULFENIC CYSTEINE, HYDROLASE, CELL CYCLE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    G.K.BUHRMAN,B.PARKER,J.SOHN,J.RUDOLPH,C.MATTOS
REVDAT   2   24-FEB-09 1YML    1       VERSN
REVDAT   1   12-APR-05 1YML    0
JRNL        AUTH   G.K.BUHRMAN,B.PARKER,J.SOHN,J.RUDOLPH,C.MATTOS
JRNL        TITL   STRUCTURAL MECHANISM OF OXIDATIVE REGULATION OF
JRNL        TITL 2 THE PHOSPHATASE CDC25B VIA AN INTRAMOLECULAR
JRNL        TITL 3 DISULFIDE BOND
JRNL        REF    BIOCHEMISTRY                  V.  44  5307 2005
JRNL        REFN                   ISSN 0006-2960
JRNL        PMID   15807524
JRNL        DOI    10.1021/BI047449FS0006-2960(04)07449-5
REMARK   1
REMARK   2
REMARK   2 RESOLUTION.    1.70 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : CNS 1.1
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK   3               : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,
REMARK   3               : READ,RICE,SIMONSON,WARREN
REMARK   3
REMARK   3  REFINEMENT TARGET : ENGH & HUBER
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 35.78
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : 377118.590
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : 0.0000
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 98.4
REMARK   3   NUMBER OF REFLECTIONS             : 29267
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) : 0.191
REMARK   3   FREE R VALUE                     : 0.208
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 10.000
REMARK   3   FREE R VALUE TEST SET COUNT      : 2919
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : 0.004
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : 6
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 1.70
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.81
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 94.90
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 4149
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2190
REMARK   3   BIN FREE R VALUE                    : 0.2440
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 10.30
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 475
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 0.011
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 1428
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 1
REMARK   3   SOLVENT ATOMS            : 172
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 19.00
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 19.60
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : 3.09000
REMARK   3    B22 (A**2) : -2.28000
REMARK   3    B33 (A**2) : -0.81000
REMARK   3    B12 (A**2) : 0.00000
REMARK   3    B13 (A**2) : 0.00000
REMARK   3    B23 (A**2) : 0.00000
REMARK   3
REMARK   3  ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 0.18
REMARK   3   ESD FROM SIGMAA              (A) : 0.06
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 5.00
REMARK   3
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : 0.20
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.10
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   BOND LENGTHS                 (A) : 0.013
REMARK   3   BOND ANGLES            (DEGREES) : 1.60
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 23.60
REMARK   3   IMPROPER ANGLES        (DEGREES) : 1.73
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) : 1.510 ; 1.500
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : 2.220 ; 2.000
REMARK   3   SIDE-CHAIN BOND              (A**2) : 2.820 ; 2.000
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : 3.600 ; 2.500
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED : FLAT MODEL
REMARK   3   KSOL        : 0.38
REMARK   3   BSOL        : 24.29
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  : PROTEIN3.PARAM
REMARK   3  PARAMETER FILE  2  : ION.PARAM
REMARK   3  PARAMETER FILE  3  : WATER_REP.PARAM
REMARK   3  PARAMETER FILE  4  : NULL
REMARK   3  TOPOLOGY FILE  1   : PROTEIN3.TOP
REMARK   3  TOPOLOGY FILE  2   : WATER.TOP
REMARK   3  TOPOLOGY FILE  3   : ION.TOP
REMARK   3  TOPOLOGY FILE  4   : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 1YML COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-05.
REMARK 100 THE RCSB ID CODE IS RCSB031688.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : NULL
REMARK 200  TEMPERATURE           (KELVIN) : 100.0
REMARK 200  PH                             : 7.25
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : APS
REMARK 200  BEAMLINE                       : 22-ID
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.0000
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : NULL
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 29267
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.700
REMARK 200  RESOLUTION RANGE LOW       (A) : 35.780
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : NULL
REMARK 200  DATA REDUNDANCY                : NULL
REMARK 200  R MERGE                    (I) : NULL
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : NULL
REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL
REMARK 200  R MERGE FOR SHELL          (I) : NULL
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: CNS
REMARK 200 STARTING MODEL: 1QB0
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 57.60
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: DTT,TRIS, AMMONIUM SULFATE, PH
REMARK 280  7.25, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 100.0K
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       24.93350
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       37.15000
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       35.54050
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       37.15000
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       24.93350
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       35.54050
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 300 REMARK: THE BIOLOGICAL UNIT IS A MONOMER
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 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     CYS A   461
REMARK 465     SER A   462
REMARK 465     LEU A   463
REMARK 465     ASP A   464
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    THR A 439       -6.41     80.87
REMARK 500    PHE A 475     -120.37   -136.36
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1001
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1YM9   RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE CDC25B PHOSPHATASE CATALYTIC
REMARK 900 DOMAIN WITH THE ACTIVE SITE CYSTEINE IN THE SULFINIC FORM
REMARK 900 RELATED ID: 1YMD   RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE CDC25B PHOSPHATASE CATALYTIC
REMARK 900 DOMAIN WITH THE ACTIVE SITE CYSTEINE IN THE SULFONIC FORM
REMARK 900 RELATED ID: 1YMK   RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE CDC25B PHOSPHATASE CATALYTIC
REMARK 900 DOMAIN IN THE APO FORM
REMARK 900 RELATED ID: 1YS0   RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE CDC25B PHOSPHATASE CATALYTIC
REMARK 900 DOMAIN WITH THE ACTIVE SITE CYSTEINE IN THE DISULFIDE FORM
DBREF  1YML A  377   550  UNP    P30305   MPIP2_HUMAN    391    564
SEQADV 1YML MET A  376  UNP  P30305              INITIATING METHIONINE
SEQADV 1YML CSO A  473  UNP  P30305    CYS   487 MODIFIED RESIDUE
SEQRES   1 A  175  MET GLU LEU ILE GLY ASP TYR SER LYS ALA PHE LEU LEU
SEQRES   2 A  175  GLN THR VAL ASP GLY LYS HIS GLN ASP LEU LYS TYR ILE
SEQRES   3 A  175  SER PRO GLU THR MET VAL ALA LEU LEU THR GLY LYS PHE
SEQRES   4 A  175  SER ASN ILE VAL ASP LYS PHE VAL ILE VAL ASP CYS ARG
SEQRES   5 A  175  TYR PRO TYR GLU TYR GLU GLY GLY HIS ILE LYS THR ALA
SEQRES   6 A  175  VAL ASN LEU PRO LEU GLU ARG ASP ALA GLU SER PHE LEU
SEQRES   7 A  175  LEU LYS SER PRO ILE ALA PRO CYS SER LEU ASP LYS ARG
SEQRES   8 A  175  VAL ILE LEU ILE PHE HIS CSO GLU PHE SER SER GLU ARG
SEQRES   9 A  175  GLY PRO ARG MET CYS ARG PHE ILE ARG GLU ARG ASP ARG
SEQRES  10 A  175  ALA VAL ASN ASP TYR PRO SER LEU TYR TYR PRO GLU MET
SEQRES  11 A  175  TYR ILE LEU LYS GLY GLY TYR LYS GLU PHE PHE PRO GLN
SEQRES  12 A  175  HIS PRO ASN PHE CYS GLU PRO GLN ASP TYR ARG PRO MET
SEQRES  13 A  175  ASN HIS GLU ALA PHE LYS ASP GLU LEU LYS THR PHE ARG
SEQRES  14 A  175  LEU LYS THR ARG SER TRP
MODRES 1YML CSO A  473  CYS  S-HYDROXYCYSTEINE
HET    CSO  A 473       7
HET     CL  A1001       1
HETNAM     CSO S-HYDROXYCYSTEINE
HETNAM      CL CHLORIDE ION
FORMUL   1  CSO    C3 H7 N O3 S
FORMUL   2   CL    CL 1-
FORMUL   3  HOH   *172(H2 O)
HELIX    1   1 SER A  402  THR A  411  1                                  10
HELIX    2   2 TYR A  428  GLY A  434  1                                   7
HELIX    3   3 LEU A  445  LYS A  455  1                                  11
HELIX    4   4 GLU A  478  VAL A  494  1                                  17
HELIX    5   5 GLY A  510  PHE A  516  1                                   7
HELIX    6   6 HIS A  519  ASN A  521  5                                   3
HELIX    7   7 HIS A  533  ALA A  535  5                                   3
HELIX    8   8 PHE A  536  LEU A  545  1                                  10
SHEET    1   A 5 TYR A 400  ILE A 401  0
SHEET    2   A 5 MET A 505  LEU A 508  1  O  ILE A 507   N  ILE A 401
SHEET    3   A 5 ARG A 466  HIS A 472  1  N  PHE A 471   O  TYR A 506
SHEET    4   A 5 VAL A 418  ASP A 425  1  N  VAL A 424   O  ILE A 470
SHEET    5   A 5 VAL A 441  ASN A 442  1  O  VAL A 441   N  ILE A 423
SHEET    1   B 2 HIS A 436  ILE A 437  0
SHEET    2   B 2 CYS A 523  GLU A 524 -1  O  GLU A 524   N  HIS A 436
LINK         C   HIS A 472                 N   CSO A 473     1555   1555  1.34
LINK         C   CSO A 473                 N   GLU A 474     1555   1555  1.33
CISPEP   1 TYR A  497    PRO A  498          0        -0.15
CISPEP   2 GLU A  524    PRO A  525          0        -1.21
SITE     1 AC1  3 HOH A 100  GLU A 446  ARG A 548
CRYST1   49.867   71.081   74.300  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      0.020053  0.000000  0.000000        0.00000
SCALE2      0.000000  0.014068  0.000000        0.00000
SCALE3      0.000000  0.000000  0.013459        0.00000
      
PROCHECK
Go to PROCHECK summary
 References