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PDBsum entry 1dg9

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Hydrolase PDB id
1dg9
Jmol
Contents
Protein chain
157 a.a. *
Ligands
EPE
* Residue conservation analysis
HEADER    HYDROLASE                               23-NOV-99   1DG9
TITLE     CRYSTAL STRUCTURE OF BOVINE LOW MOLECULAR WEIGHT PTPASE
TITLE    2 COMPLEXED WITH HEPES
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: TYROSINE PHOSPHATASE;
COMPND   3 CHAIN: A;
COMPND   4 EC: 3.1.3.48;
COMPND   5 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: BOS TAURUS;
SOURCE   3 ORGANISM_COMMON: CATTLE;
SOURCE   4 ORGANISM_TAXID: 9913;
SOURCE   5 ORGAN: HEART;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   8 EXPRESSION_SYSTEM_PLASMID: PET
KEYWDS    PTPASE, HEPES COMPLEX, HYDROLASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    M.ZHANG,M.ZHOU,R.L.VAN ETTEN,C.V.STAUFFACHER
REVDAT   3   24-FEB-09 1DG9    1       VERSN
REVDAT   2   15-MAR-05 1DG9    1       REMARK
REVDAT   1   08-DEC-99 1DG9    0
JRNL        AUTH   M.ZHANG,M.ZHOU,R.L.VAN ETTEN,C.V.STAUFFACHER
JRNL        TITL   CRYSTAL STRUCTURE OF BOVINE LOW MOLECULAR WEIGHT
JRNL        TITL 2 PHOSPHOTYROSYL PHOSPHATASE COMPLEXED WITH THE
JRNL        TITL 3 TRANSITION STATE ANALOG VANADATE.
JRNL        REF    BIOCHEMISTRY                  V.  36    15 1997
JRNL        REFN                   ISSN 0006-2960
JRNL        PMID   8993313
JRNL        DOI    10.1021/BI961804N
REMARK   1
REMARK   2
REMARK   2 RESOLUTION.    1.90 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : TNT
REMARK   3   AUTHORS     : TRONRUD,TEN EYCK,MATTHEWS
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   COMPLETENESS FOR RANGE        (%) : NULL
REMARK   3   NUMBER OF REFLECTIONS             : 11869
REMARK   3
REMARK   3  USING DATA ABOVE SIGMA CUTOFF.
REMARK   3   CROSS-VALIDATION METHOD          : NULL
REMARK   3   FREE R VALUE TEST SET SELECTION  : NULL
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.179
REMARK   3   R VALUE            (WORKING SET) : NULL
REMARK   3   FREE R VALUE                     : NULL
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT      : NULL
REMARK   3
REMARK   3  USING ALL DATA, NO SIGMA CUTOFF.
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : NULL
REMARK   3   FREE R VALUE                  (NO CUTOFF) : NULL
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : NULL
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : NULL
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 1256
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 15
REMARK   3   SOLVENT ATOMS            : 0
REMARK   3
REMARK   3  WILSON B VALUE (FROM FCALC, A**2) : NULL
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.    RMS    WEIGHT  COUNT
REMARK   3   BOND LENGTHS                 (A) : 0.010 ; NULL  ; NULL
REMARK   3   BOND ANGLES            (DEGREES) : 2.340 ; NULL  ; NULL
REMARK   3   TORSION ANGLES         (DEGREES) : NULL  ; NULL  ; NULL
REMARK   3   PSEUDOROTATION ANGLES  (DEGREES) : NULL  ; NULL  ; NULL
REMARK   3   TRIGONAL CARBON PLANES       (A) : NULL  ; NULL  ; NULL
REMARK   3   GENERAL PLANES               (A) : NULL  ; NULL  ; NULL
REMARK   3   ISOTROPIC THERMAL FACTORS (A**2) : NULL  ; NULL  ; NULL
REMARK   3   NON-BONDED CONTACTS          (A) : NULL  ; NULL  ; NULL
REMARK   3
REMARK   3  INCORRECT CHIRAL-CENTERS (COUNT) : NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED : NULL
REMARK   3   KSOL        : NULL
REMARK   3   BSOL        : NULL
REMARK   3
REMARK   3  RESTRAINT LIBRARIES.
REMARK   3   STEREOCHEMISTRY : ENGH & HUBER
REMARK   3   ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 1DG9 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-NOV-99.
REMARK 100 THE RCSB ID CODE IS RCSB010061.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 01-JAN-96
REMARK 200  TEMPERATURE           (KELVIN) : 298.0
REMARK 200  PH                             : 7.5
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 RU200
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.5418
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU RAXIS II
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : R-AXIS
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 71205
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.900
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                : NULL
REMARK 200  R MERGE                    (I) : 0.06500
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) : 1.90
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: NULL
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 43.54
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG4K, 10% 2-PROPANOL, 100MM
REMARK 280  HEPES, PH 7.5, VAPOR DIFFUSION
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,Y,-Z
REMARK 290       3555   X+1/2,Y+1/2,Z
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        0.00000
REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   3  1.000000  0.000000  0.000000       47.65000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       21.70000
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   4 -1.000000  0.000000  0.000000       47.65000
REMARK 290   SMTRY2   4  0.000000  1.000000  0.000000       21.70000
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 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 LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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   RES CSSEQI ATM2   DEVIATION
REMARK 500    GLU A  93   CD    GLU A  93   OE2     0.068
REMARK 500    GLU A 154   CD    GLU A 154   OE2     0.086
REMARK 500
REMARK 500 REMARK: NULL
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    CYS A  12   N   -  CA  -  CB  ANGL. DEV. =   9.3 DEGREES
REMARK 500    ASP A  37   CB  -  CG  -  OD1 ANGL. DEV. =   7.6 DEGREES
REMARK 500    ASP A  37   CB  -  CG  -  OD2 ANGL. DEV. =  -6.3 DEGREES
REMARK 500    ASP A  42   CB  -  CG  -  OD1 ANGL. DEV. =   7.8 DEGREES
REMARK 500    ASP A  42   CB  -  CG  -  OD2 ANGL. DEV. =  -7.8 DEGREES
REMARK 500    ASP A  56   CB  -  CG  -  OD1 ANGL. DEV. =   7.5 DEGREES
REMARK 500    ASP A  56   CB  -  CG  -  OD2 ANGL. DEV. =  -6.9 DEGREES
REMARK 500    ARG A  58   NE  -  CZ  -  NH1 ANGL. DEV. =  -3.3 DEGREES
REMARK 500    ASP A 120   CB  -  CG  -  OD1 ANGL. DEV. =   6.2 DEGREES
REMARK 500    ARG A 147   NE  -  CZ  -  NH1 ANGL. DEV. =   4.3 DEGREES
REMARK 500    ARG A 147   NE  -  CZ  -  NH2 ANGL. DEV. =  -6.2 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    GLN A   3     -148.25   -164.54
REMARK 500    ASN A 108       54.13   -105.49
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 EPE A 201
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1PNT   RELATED DB: PDB
REMARK 900 1PNT CONTAINS THE SAME PROTEIN COMPLEXED WITH PO4
REMARK 900 RELATED ID: 2PNT   RELATED DB: PDB
REMARK 900 THIS IS THE ID CODE USED IN THE PRIMARY CITATION.
DBREF  1DG9 A    1   157  UNP    P11064   PPAC_BOVIN       1    157
SEQRES   1 A  157  ALA GLU GLN VAL THR LYS SER VAL LEU PHE VAL CYS LEU
SEQRES   2 A  157  GLY ASN ILE CYS ARG SER PRO ILE ALA GLU ALA VAL PHE
SEQRES   3 A  157  ARG LYS LEU VAL THR ASP GLN ASN ILE SER ASP ASN TRP
SEQRES   4 A  157  VAL ILE ASP SER GLY ALA VAL SER ASP TRP ASN VAL GLY
SEQRES   5 A  157  ARG SER PRO ASP PRO ARG ALA VAL SER CYS LEU ARG ASN
SEQRES   6 A  157  HIS GLY ILE ASN THR ALA HIS LYS ALA ARG GLN VAL THR
SEQRES   7 A  157  LYS GLU ASP PHE VAL THR PHE ASP TYR ILE LEU CYS MET
SEQRES   8 A  157  ASP GLU SER ASN LEU ARG ASP LEU ASN ARG LYS SER ASN
SEQRES   9 A  157  GLN VAL LYS ASN CYS ARG ALA LYS ILE GLU LEU LEU GLY
SEQRES  10 A  157  SER TYR ASP PRO GLN LYS GLN LEU ILE ILE GLU ASP PRO
SEQRES  11 A  157  TYR TYR GLY ASN ASP ALA ASP PHE GLU THR VAL TYR GLN
SEQRES  12 A  157  GLN CYS VAL ARG CYS CYS ARG ALA PHE LEU GLU LYS VAL
SEQRES  13 A  157  ARG
HET    EPE  A 201      15
HETNAM     EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HETSYN     EPE HEPES
FORMUL   2  EPE    C8 H18 N2 O4 S
HELIX    1   1 CYS A   17  GLN A   33  1                                  17
HELIX    2   2 ILE A   35  ASP A   37  5                                   3
HELIX    3   3 ASP A   56  HIS A   66  1                                  11
HELIX    4   4 GLU A   80  PHE A   85  1                                   6
HELIX    5   5 ASP A   92  ASN A  104  1                                  13
HELIX    6   6 GLY A  117  ASP A  120  5                                   4
HELIX    7   7 ASN A  134  ARG A  157  1                                  24
SHEET    1   A 4 TRP A  39  ALA A  45  0
SHEET    2   A 4 LYS A   6  CYS A  12  1  O  LYS A   6   N  VAL A  40
SHEET    3   A 4 TYR A  87  CYS A  90  1  O  TYR A  87   N  LEU A   9
SHEET    4   A 4 LYS A 112  LEU A 115  1  O  LYS A 112   N  ILE A  88
SITE     1 AC1 10 CYS A  12  LEU A  13  GLY A  14  ASN A  15
SITE     2 AC1 10 ILE A  16  CYS A  17  ARG A  18  ASP A 129
SITE     3 AC1 10 TYR A 131  TYR A 132
CRYST1   95.300   43.400   41.200  90.00 113.40  90.00 C 1 2 1       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      0.010493  0.000000  0.004541        0.00000
SCALE2      0.000000  0.023041  0.000000        0.00000
SCALE3      0.000000  0.000000  0.026447        0.00000
      
PROCHECK
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 References