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PDBsum entry 2fek

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Hydrolase PDB id
2fek
Jmol
Contents
Protein chain
147 a.a.
HEADER    HYDROLASE                               16-DEC-05   2FEK
TITLE     STRUCTURE OF A PROTEIN TYROSINE PHOSPHATASE
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: LOW MOLECULAR WEIGHT PROTEIN-TYROSINE-
COMPND   3 PHOSPHATASE WZB;
COMPND   4 CHAIN: A;
COMPND   5 EC: 3.1.3.48;
COMPND   6 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12;
SOURCE   3 ORGANISM_TAXID: 83333;
SOURCE   4 STRAIN: K-12;
SOURCE   5 GENE: WZB;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE  10 EXPRESSION_SYSTEM_PLASMID: PET28A
KEYWDS    LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE,
KEYWDS   2 ESCHERICHIA COLI, PHOSPHATE BINDING, HYDROLASE
EXPDTA    SOLUTION NMR
NUMMDL    20
AUTHOR    E.LESCOP,C.JIN
REVDAT   3   24-FEB-09 2FEK    1       VERSN
REVDAT   2   26-SEP-06 2FEK    1       JRNL
REVDAT   1   09-MAY-06 2FEK    0
JRNL        AUTH   E.LESCOP,Y.HU,H.XU,W.HU,J.CHEN,B.XIA,C.JIN
JRNL        TITL   THE SOLUTION STRUCTURE OF ESCHERICHIA COLI WZB
JRNL        TITL 2 REVEALS A NOVEL SUBSTRATE RECOGNITION MECHANISM OF
JRNL        TITL 3 PROKARYOTIC LOW MOLECULAR WEIGHT PROTEIN-TYROSINE
JRNL        TITL 4 PHOSPHATASES
JRNL        REF    J.BIOL.CHEM.                  V. 281 19570 2006
JRNL        REFN                   ISSN 0021-9258
JRNL        PMID   16651264
JRNL        DOI    10.1074/JBC.M601263200
REMARK   1
REMARK   2
REMARK   2 RESOLUTION. NOT APPLICABLE.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : AMBER 7
REMARK   3   AUTHORS     : CASE
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: A TOTAL OF 4689 RESTRAINTS WERE
REMARK   3  USED. INCLUDED ARE 1630 AMBIGUOUS AND 2640 UNAMBIGUOUS NOE-
REMARK   3  DERIVED DISTANCES, 100 HYDROGEN BOND RESTRAINTS, 190 BACKBONE
REMARK   3  DIHEDRAL ANGLES, 32 SIDE-CHAIN CHI1 AND 97 1H-15N RESIDUAL
REMARK   3  DIPOLAR COUPLINGS VALUES.
REMARK   4
REMARK   4 2FEK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-DEC-05.
REMARK 100 THE RCSB ID CODE IS RCSB035783.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210  EXPERIMENT TYPE                : NMR
REMARK 210  TEMPERATURE           (KELVIN) : 298
REMARK 210  PH                             : 6
REMARK 210  IONIC STRENGTH                 : 100MM
REMARK 210  PRESSURE                       : AMBIENT
REMARK 210  SAMPLE CONTENTS                : ~1MM WZB U-15N, 13C; 50MM
REMARK 210                                   SODIUM PHOSPHATE, 50MM NACL
REMARK 210                                   BUFFER; 25MM DTT; 5MM EDTA; PH
REMARK 210                                   6; ~1MM WZB U-15N; 50MM SODIUM
REMARK 210                                   PHOSPHATE, 50MM NACL BUFFER;
REMARK 210                                   25MM DTT; 5MM EDTA; PH 6
REMARK 210
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 3D_13C-SEPARATED_NOESY, 3D_
REMARK 210                                   15N-SEPARATED_NOESY
REMARK 210  SPECTROMETER FIELD STRENGTH    : 800 MHZ, 500 MHZ
REMARK 210  SPECTROMETER MODEL             : AVANCE
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER
REMARK 210
REMARK 210  STRUCTURE DETERMINATION.
REMARK 210   SOFTWARE USED                 : XWINNMR 3.5, NMRPIPE 1, CYANA
REMARK 210                                   1.2, NMRVIEW 5
REMARK 210   METHOD USED                   : 200 STRUCTURES WERE GENERATED
REMARK 210                                   IN CYANA. THE 100 STRUCTURES
REMARK 210                                   WITH LOWEST ENERGY WERE
REMARK 210                                   FURTHER REFINED IN AMBER7. THE
REMARK 210                                   20 LOWEST ENERGY STRUCTURES
REMARK 210                                   WERE FINALLY SELECTED.
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH LOWEST ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: 97 1H-15N RESIDUAL DIPOLAR, MEASURED IN PEG/HEXANOL
REMARK 210  (5.5 WT%, MOLAR RATIO=0.92), WERE INCLUDED IN STRUCTURE
REMARK 210  CALCULATION.
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA.  PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465   MODELS 1-20
REMARK 465     RES C SSSEQI
REMARK 465     MET A   -19
REMARK 465     GLY A   -18
REMARK 465     SER A   -17
REMARK 465     SER A   -16
REMARK 465     HIS A   -15
REMARK 465     HIS A   -14
REMARK 465     HIS A   -13
REMARK 465     HIS A   -12
REMARK 465     HIS A   -11
REMARK 465     HIS A   -10
REMARK 465     SER A    -9
REMARK 465     SER A    -8
REMARK 465     GLY A    -7
REMARK 465     LEU A    -6
REMARK 465     VAL A    -5
REMARK 465     PRO A    -4
REMARK 465     ARG A    -3
REMARK 465     GLY A    -2
REMARK 465     SER A    -1
REMARK 465     HIS A     0
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  6 ARG A  66   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.6 DEGREES
REMARK 500  6 ARG A  89   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.1 DEGREES
REMARK 500  8 ARG A  89   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.1 DEGREES
REMARK 500  9 ARG A  85   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.4 DEGREES
REMARK 500 12 ARG A  85   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.3 DEGREES
REMARK 500 17 ARG A  74   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.1 DEGREES
REMARK 500 18 ARG A  21   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.7 DEGREES
REMARK 500 18 ARG A  66   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.4 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  1 ASN A  12      -49.33     77.52
REMARK 500  1 ILE A  13       -5.26    -58.26
REMARK 500  1 CYS A  14      -75.90   -126.28
REMARK 500  1 LEU A  40       57.63   -101.47
REMARK 500  1 LEU A  60       25.05    -77.93
REMARK 500  1 TYR A 117      -85.81     22.64
REMARK 500  1 ALA A 144     -157.02    -77.75
REMARK 500  2 PHE A   2       58.42    -67.90
REMARK 500  2 ASN A  12      -50.44     71.11
REMARK 500  2 CYS A  14      -75.08   -117.11
REMARK 500  2 LEU A  60       22.87    -78.11
REMARK 500  2 PRO A 114      172.09    -57.28
REMARK 500  3 CYS A  14      -42.02   -135.84
REMARK 500  3 ALA A  35     -168.64   -163.14
REMARK 500  3 PRO A 114      176.82    -57.62
REMARK 500  4 ASN A  12      -36.70     67.39
REMARK 500  4 ILE A  13        0.83    -60.48
REMARK 500  4 CYS A  14      -63.20   -147.74
REMARK 500  4 LEU A  40       76.37   -114.61
REMARK 500  4 ASP A 108       59.83    -91.29
REMARK 500  5 ASN A  12      -39.97     66.03
REMARK 500  5 CYS A  14      -78.84   -128.04
REMARK 500  5 TYR A 117      -95.55     22.45
REMARK 500  5 GLU A 145       26.77     39.74
REMARK 500  6 ASN A   3      -19.22     52.68
REMARK 500  6 ASN A  12      -58.75     65.47
REMARK 500  6 ARG A  15      -45.16   -139.24
REMARK 500  6 PRO A 114      171.86    -56.55
REMARK 500  6 TYR A 117      -67.65    -20.18
REMARK 500  6 GLU A 145       36.41     39.77
REMARK 500  7 ASN A   3      -46.70     68.85
REMARK 500  7 ASN A  12      -55.10     66.62
REMARK 500  7 ILE A  13        6.49    -58.39
REMARK 500  7 CYS A  14      -64.86   -139.14
REMARK 500  7 PRO A 114      171.02    -55.40
REMARK 500  7 TYR A 117      -69.82      2.38
REMARK 500  7 GLU A 145       32.64   -152.91
REMARK 500  8 PHE A   2       50.80    -68.37
REMARK 500  8 ASN A  12      -50.46     64.02
REMARK 500  8 CYS A  14      -69.76   -124.88
REMARK 500  9 ASN A  12      -49.05     71.66
REMARK 500  9 ILE A  13        2.05    -65.65
REMARK 500  9 CYS A  14      -73.96   -121.10
REMARK 500  9 LEU A  40       68.17   -116.80
REMARK 500  9 PRO A 114      171.65    -59.56
REMARK 500  9 ALA A 144     -152.39    -77.52
REMARK 500 10 ASN A  12      -58.46     67.39
REMARK 500 10 ILE A  13        0.33    -60.71
REMARK 500 10 ARG A  15      -49.75   -135.45
REMARK 500 10 LEU A  40       67.27   -109.31
REMARK 500 10 VAL A  41      125.78    -38.14
REMARK 500 11 PHE A   2       99.84    -69.28
REMARK 500 11 ILE A  13       -9.04    -56.69
REMARK 500 11 CYS A  14      -52.73   -131.14
REMARK 500 11 PRO A 114      174.15    -56.68
REMARK 500 11 GLU A 145       40.80     39.86
REMARK 500 12 ASN A  12      -45.08     73.36
REMARK 500 12 ILE A  13        2.30    -65.40
REMARK 500 12 CYS A  14      -79.82   -121.11
REMARK 500 12 LEU A  40       70.86   -118.55
REMARK 500 12 GLU A 145       51.42    -91.36
REMARK 500 13 ASN A   3      -40.87     63.00
REMARK 500 13 CYS A  14      -67.19   -130.22
REMARK 500 13 GLU A  61      -68.47     68.33
REMARK 500 13 TYR A 117      -85.92     32.43
REMARK 500 13 ALA A 144       36.05   -146.69
REMARK 500 14 ASN A  12      -44.54     73.44
REMARK 500 14 ILE A  13       -5.89    -58.89
REMARK 500 14 CYS A  14      -67.57   -131.22
REMARK 500 14 ASP A 108       45.28   -101.96
REMARK 500 14 PRO A 114      173.00    -55.48
REMARK 500 14 TYR A 117      -84.30     12.84
REMARK 500 15 PHE A   2       46.17    -68.49
REMARK 500 15 ASN A  12      -14.26     63.00
REMARK 500 15 ILE A  13       -3.10    -58.92
REMARK 500 15 CYS A  14      -75.48   -144.54
REMARK 500 15 LEU A  40       73.75   -102.21
REMARK 500 15 SER A  59       56.64    -94.96
REMARK 500 15 ASP A 108       36.36    -97.56
REMARK 500 15 TYR A 117      -87.67     20.59
REMARK 500 16 ASN A  12      -45.86     67.94
REMARK 500 16 CYS A  14      -76.77   -125.92
REMARK 500 16 LEU A  40       77.81   -117.64
REMARK 500 16 TYR A 117      -68.44    -12.20
REMARK 500 17 ASN A  12      -47.02     70.74
REMARK 500 17 ILE A  13       -8.97    -55.89
REMARK 500 17 CYS A  14      -70.43   -126.91
REMARK 500 17 LEU A  40       66.70   -116.60
REMARK 500 17 TYR A 117      -90.97     27.88
REMARK 500 17 ALA A 144     -153.58   -120.30
REMARK 500 18 ASN A   3      -46.79     60.41
REMARK 500 18 CYS A  14      -50.67   -141.28
REMARK 500 18 GLU A  61      170.45    -57.75
REMARK 500 18 PRO A 114      173.86    -56.82
REMARK 500 18 GLU A 145       32.76   -141.89
REMARK 500 19 ASN A  12      -48.52     68.10
REMARK 500 19 ILE A  13       13.81    -65.72
REMARK 500 19 CYS A  14      -80.92   -137.86
REMARK 500 19 PRO A 114      175.60    -58.05
REMARK 500 19 TYR A 117      -37.76    -39.92
REMARK 500 19 ALA A 144       23.90   -144.20
REMARK 500 20 PHE A   2       44.38    -72.77
REMARK 500 20 ASN A  12      -49.25     68.89
REMARK 500 20 ILE A  13       -6.00    -56.49
REMARK 500 20 CYS A  14      -80.05   -116.95
REMARK 500 20 LEU A  40       76.47   -112.75
REMARK 500 20 GLU A  61     -146.02     51.76
REMARK 500 20 ALA A 144       27.19   -144.72
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500  M RES CSSEQI        RMS     TYPE
REMARK 500  5 ARG A  66         0.09    SIDE_CHAIN
REMARK 500  6 TYR A 128         0.07    SIDE_CHAIN
REMARK 500 13 ARG A  21         0.10    SIDE_CHAIN
REMARK 500 13 ARG A  85         0.09    SIDE_CHAIN
REMARK 500 14 ARG A  70         0.09    SIDE_CHAIN
REMARK 500 15 TYR A  76         0.08    SIDE_CHAIN
REMARK 500 15 ARG A 118         0.08    SIDE_CHAIN
REMARK 500 17 ARG A  85         0.11    SIDE_CHAIN
REMARK 500 18 ARG A  85         0.12    SIDE_CHAIN
REMARK 500 19 TYR A 128         0.08    SIDE_CHAIN
REMARK 500
REMARK 500 REMARK: NULL
DBREF  2FEK A    1   147  UNP    P0AAB2   WZB_ECOLI        1    147
SEQADV 2FEK MET A  -19  UNP  P0AAB2              EXPRESSION TAG
SEQADV 2FEK GLY A  -18  UNP  P0AAB2              EXPRESSION TAG
SEQADV 2FEK SER A  -17  UNP  P0AAB2              EXPRESSION TAG
SEQADV 2FEK SER A  -16  UNP  P0AAB2              EXPRESSION TAG
SEQADV 2FEK HIS A  -15  UNP  P0AAB2              EXPRESSION TAG
SEQADV 2FEK HIS A  -14  UNP  P0AAB2              EXPRESSION TAG
SEQADV 2FEK HIS A  -13  UNP  P0AAB2              EXPRESSION TAG
SEQADV 2FEK HIS A  -12  UNP  P0AAB2              EXPRESSION TAG
SEQADV 2FEK HIS A  -11  UNP  P0AAB2              EXPRESSION TAG
SEQADV 2FEK HIS A  -10  UNP  P0AAB2              EXPRESSION TAG
SEQADV 2FEK SER A   -9  UNP  P0AAB2              EXPRESSION TAG
SEQADV 2FEK SER A   -8  UNP  P0AAB2              EXPRESSION TAG
SEQADV 2FEK GLY A   -7  UNP  P0AAB2              EXPRESSION TAG
SEQADV 2FEK LEU A   -6  UNP  P0AAB2              EXPRESSION TAG
SEQADV 2FEK VAL A   -5  UNP  P0AAB2              EXPRESSION TAG
SEQADV 2FEK PRO A   -4  UNP  P0AAB2              EXPRESSION TAG
SEQADV 2FEK ARG A   -3  UNP  P0AAB2              EXPRESSION TAG
SEQADV 2FEK GLY A   -2  UNP  P0AAB2              EXPRESSION TAG
SEQADV 2FEK SER A   -1  UNP  P0AAB2              EXPRESSION TAG
SEQADV 2FEK HIS A    0  UNP  P0AAB2              EXPRESSION TAG
SEQRES   1 A  167  MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY
SEQRES   2 A  167  LEU VAL PRO ARG GLY SER HIS MET PHE ASN ASN ILE LEU
SEQRES   3 A  167  VAL VAL CYS VAL GLY ASN ILE CYS ARG SER PRO THR ALA
SEQRES   4 A  167  GLU ARG LEU LEU GLN ARG TYR HIS PRO GLU LEU LYS VAL
SEQRES   5 A  167  GLU SER ALA GLY LEU GLY ALA LEU VAL GLY LYS GLY ALA
SEQRES   6 A  167  ASP PRO THR ALA ILE SER VAL ALA ALA GLU HIS GLN LEU
SEQRES   7 A  167  SER LEU GLU GLY HIS CYS ALA ARG GLN ILE SER ARG ARG
SEQRES   8 A  167  LEU CYS ARG ASN TYR ASP LEU ILE LEU THR MET GLU LYS
SEQRES   9 A  167  ARG HIS ILE GLU ARG LEU CYS GLU MET ALA PRO GLU MET
SEQRES  10 A  167  ARG GLY LYS VAL MET LEU PHE GLY HIS TRP ASP ASN GLU
SEQRES  11 A  167  CYS GLU ILE PRO ASP PRO TYR ARG LYS SER ARG GLU THR
SEQRES  12 A  167  PHE ALA ALA VAL TYR THR LEU LEU GLU ARG SER ALA ARG
SEQRES  13 A  167  GLN TRP ALA GLN ALA LEU ASN ALA GLU GLN VAL
HELIX    1   1 CYS A   14  HIS A   27  1                                  14
HELIX    2   2 ASP A   46  HIS A   56  1                                  11
HELIX    3   3 SER A   69  TYR A   76  1                                   8
HELIX    4   4 GLU A   83  ALA A   94  1                                  12
HELIX    5   5 PRO A   95  GLY A   99  5                                   5
HELIX    6   6 GLY A  105  ASP A  108  5                                   4
HELIX    7   7 SER A  120  ALA A  144  1                                  25
SHEET    1   A 4 LYS A  31  GLY A  36  0
SHEET    2   A 4 ASN A   4  CYS A   9  1  N  VAL A   7   O  ALA A  35
SHEET    3   A 4 LEU A  78  THR A  81  1  O  LEU A  80   N  LEU A   6
SHEET    4   A 4 VAL A 101  LEU A 103  1  O  MET A 102   N  ILE A  79
CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1
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      1.000000  0.000000  0.000000        0.00000
SCALE2      0.000000  1.000000  0.000000        0.00000
SCALE3      0.000000  0.000000  1.000000        0.00000
      
PROCHECK
Go to PROCHECK summary
 References