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PDBsum entry 2kgj

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Isomerase PDB id
2kgj
Jmol
Contents
Protein chain
102 a.a.
HEADER    ISOMERASE                               12-MAR-09   2KGJ
TITLE     SOLUTION STRUCTURE OF PARVULIN DOMAIN OF PPID FROM E.COLI
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE D;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: UNP RESIDUES 264-357;
COMPND   5 SYNONYM: PPIASE D, ROTAMASE D;
COMPND   6 EC: 5.2.1.8;
COMPND   7 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE   3 ORGANISM_TAXID: 83333;
SOURCE   4 STRAIN: K12;
SOURCE   5 GENE: PPID, YBAU, B0441, JW0431;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR;
SOURCE  10 EXPRESSION_SYSTEM_VECTOR: PET 11A
KEYWDS    PROLYL ISOMERASE, PARVULIN, CELL INNER MEMBRANE, CELL
KEYWDS   2 MEMBRANE, ISOMERASE, MEMBRANE, ROTAMASE, STRESS RESPONSE,
KEYWDS   3 TRANSMEMBRANE
EXPDTA    SOLUTION NMR
NUMMDL    10
AUTHOR    U.WEININGER,R.P.JAKOB
REVDAT   1   19-JAN-10 2KGJ    0
JRNL        AUTH   U.WEININGER,R.P.JAKOB,M.KOVERMANN,J.BALBACH,
JRNL        AUTH 2 F.X.SCHMID
JRNL        TITL   THE PROLYL ISOMERASE DOMAIN OF PPID FROM
JRNL        TITL 2 ESCHERICHIA COLI SHOWS A PARVULIN FOLD BUT IS
JRNL        TITL 3 DEVOID OF CATALYTIC ACTIVITY.
JRNL        REF    PROTEIN SCI.                  V.  19     6 2009
JRNL        REFN                   ISSN 0961-8368
JRNL        PMID   19866485
JRNL        DOI    10.1002/PRO.277
REMARK   1
REMARK   2
REMARK   2 RESOLUTION. NOT APPLICABLE.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : ARIA 2.0
REMARK   3   AUTHORS     : LINGE, O'DONOGHUE AND NILGES
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 2KGJ COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-APR-09.
REMARK 100 THE RCSB ID CODE IS RCSB101092.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210  EXPERIMENT TYPE                : NMR
REMARK 210  TEMPERATURE           (KELVIN) : 298
REMARK 210  PH                             : 7.0
REMARK 210  IONIC STRENGTH                 : 0.1
REMARK 210  PRESSURE                       : AMBIENT
REMARK 210  SAMPLE CONTENTS                : 100 MM POTASSIUM PHOSPHATE-1,
REMARK 210                                   5 MM [U-15N] PROTEIN, 90% H2O/
REMARK 210                                   10% D2O
REMARK 210
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D 1H-15N HSQC; 3D 1H-15N
REMARK 210                                   NOESY; 3D 1H-15N TOCSY; 2D 1H-
REMARK 210                                   1H NOESY
REMARK 210  SPECTROMETER FIELD STRENGTH    : 800 MHZ
REMARK 210  SPECTROMETER MODEL             : AVANCE
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER
REMARK 210
REMARK 210  STRUCTURE DETERMINATION.
REMARK 210   SOFTWARE USED                 : ARIA 2.0
REMARK 210   METHOD USED                   : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE LOWEST
REMARK 210                                   ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: NULL
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 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
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   HD2  TYR A     8    HD21  LEU A    55              1.38
REMARK 500   HA   ILE A    43     HB2  ALA A    46              1.40
REMARK 500  HD13  LEU A    26    HD11  LEU A    75              1.51
REMARK 500   HB2  ALA A    67    HG13  VAL A    88              1.54
REMARK 500   HE1  TYR A     8     HB2  LEU A    69              1.57
REMARK 500   OE2  GLU A    18     HZ1  LYS A    39              1.57
REMARK 500   HB3  LEU A    75     HG3  ARG A    89              1.58
REMARK 500   HG2  LYS A    80     HE2  PHE A    85              1.59
REMARK 500   HG   SER A    40     HB3  ASP A    42              1.59
REMARK 500   HA   LEU A    23     HG   LEU A    26              1.59
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 SER A  76       53.24     77.99
REMARK 500  1 ALA A  96      -66.55     72.01
REMARK 500  1 HIS A  98       95.30    -68.72
REMARK 500  1 HIS A  99      -64.99   -179.76
REMARK 500  1 HIS A 100      -59.65   -149.02
REMARK 500  1 HIS A 101      114.23   -162.99
REMARK 500  2 SER A  76       60.37     78.64
REMARK 500  2 ALA A  96      -84.33     63.76
REMARK 500  2 HIS A  98       49.90    -98.05
REMARK 500  2 HIS A  99       87.73     53.93
REMARK 500  2 HIS A 100      -27.23     75.05
REMARK 500  3 SER A  76       46.20     78.56
REMARK 500  3 ALA A  96      -75.89   -112.21
REMARK 500  3 HIS A  98      -78.03   -128.75
REMARK 500  3 HIS A  99      -39.15   -146.27
REMARK 500  3 HIS A 101       93.06    -69.38
REMARK 500  4 SER A  76       45.79     78.10
REMARK 500  4 ALA A  95      -37.38     73.27
REMARK 500  4 ALA A  96      102.17    -52.80
REMARK 500  4 HIS A  97       -6.54     70.79
REMARK 500  5 SER A  76       56.12     78.49
REMARK 500  5 ALA A  95       34.41    -90.31
REMARK 500  5 ALA A  96      -61.39     71.32
REMARK 500  5 HIS A  99      -74.05   -116.42
REMARK 500  5 HIS A 100      -72.52   -118.01
REMARK 500  6 LYS A  70      -60.10   -102.66
REMARK 500  6 SER A  76       45.71     78.15
REMARK 500  6 HIS A  97      115.40     75.35
REMARK 500  6 HIS A  98      -44.81   -145.73
REMARK 500  6 HIS A  99      -72.54   -176.29
REMARK 500  7 SER A  76       57.82     76.33
REMARK 500  7 ALA A  95       45.42    -85.02
REMARK 500  7 ALA A  96     -162.27     63.23
REMARK 500  7 HIS A  97      -99.71    -94.31
REMARK 500  7 HIS A  98      -72.70     62.35
REMARK 500  7 HIS A  99      -14.53   -153.96
REMARK 500  8 SER A  76       59.98     78.87
REMARK 500  8 HIS A  97      -44.36     74.87
REMARK 500  9 SER A  76       60.95     78.98
REMARK 500  9 ALA A  96       85.06     56.08
REMARK 500  9 HIS A  97     -142.98     69.21
REMARK 500  9 HIS A  98      -47.17     74.49
REMARK 500  9 HIS A 101       24.28   -161.12
REMARK 500 10 SER A  76       49.71     79.25
REMARK 500 10 ALA A  95      -53.29     72.83
REMARK 500 10 HIS A 101       75.85     54.40
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 16211   RELATED DB: BMRB
DBREF  2KGJ A    1    94  UNP    P0ADY1   PPID_ECOLI     264    357
SEQADV 2KGJ ALA A   95  UNP  P0ADY1              EXPRESSION TAG
SEQADV 2KGJ ALA A   96  UNP  P0ADY1              EXPRESSION TAG
SEQADV 2KGJ HIS A   97  UNP  P0ADY1              EXPRESSION TAG
SEQADV 2KGJ HIS A   98  UNP  P0ADY1              EXPRESSION TAG
SEQADV 2KGJ HIS A   99  UNP  P0ADY1              EXPRESSION TAG
SEQADV 2KGJ HIS A  100  UNP  P0ADY1              EXPRESSION TAG
SEQADV 2KGJ HIS A  101  UNP  P0ADY1              EXPRESSION TAG
SEQADV 2KGJ HIS A  102  UNP  P0ADY1              EXPRESSION TAG
SEQRES   1 A  102  THR GLN PRO GLN ARG THR ARG TYR SER ILE ILE GLN THR
SEQRES   2 A  102  LYS THR GLU ASP GLU ALA LYS ALA VAL LEU ASP GLU LEU
SEQRES   3 A  102  ASN LYS GLY GLY ASP PHE ALA ALA LEU ALA LYS GLU LYS
SEQRES   4 A  102  SER ALA ASP ILE ILE SER ALA ARG ASN GLY GLY ASP MET
SEQRES   5 A  102  GLY TRP LEU GLU ASP ALA THR ILE PRO ASP GLU LEU LYS
SEQRES   6 A  102  ASN ALA GLY LEU LYS GLU LYS GLY GLN LEU SER GLY VAL
SEQRES   7 A  102  ILE LYS SER SER VAL GLY PHE LEU ILE VAL ARG LEU ASP
SEQRES   8 A  102  ASP ILE GLN ALA ALA HIS HIS HIS HIS HIS HIS
HELIX    1   1 THR A   15  GLY A   29  1                                  15
HELIX    2   2 ASP A   31  LYS A   39  1                                   9
HELIX    3   3 ASP A   42  ARG A   47  1                                   6
HELIX    4   4 PRO A   61  ASN A   66  1                                   6
SHEET    1   A 4 ASP A  51  GLU A  56  0
SHEET    2   A 4 ARG A   5  THR A  13 -1  N  THR A   6   O  LEU A  55
SHEET    3   A 4 GLY A  84  GLN A  94 -1  O  PHE A  85   N  THR A  13
SHEET    4   A 4 LEU A  75  SER A  81 -1  N  ILE A  79   O  LEU A  86
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
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 References