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PDBsum entry 2kr7

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Isomerase PDB id
2kr7
Jmol
Contents
Protein chain
151 a.a.
HEADER    ISOMERASE                               07-DEC-09   2KR7
TITLE     SOLUTION STRUCTURE OF HELICOBACTER PYLORI SLYD
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: FKBP-TYPE PEPTIDYL-PROLYL CIS-TRANS ISOMERASE SLYD;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: UNP RESIDUES 1-151;
COMPND   5 SYNONYM: PPIASE, ROTAMASE;
COMPND   6 EC: 5.2.1.8;
COMPND   7 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI;
SOURCE   3 ORGANISM_COMMON: CAMPYLOBACTER PYLORI;
SOURCE   4 ORGANISM_TAXID: 210;
SOURCE   5 STRAIN: 26695;
SOURCE   6 GENE: SLYD, HP_1123;
SOURCE   7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   8 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE  10 EXPRESSION_SYSTEM_VECTOR: PET-32A(+)
KEYWDS    PROTEIN, ISOMERASE, ROTAMASE
EXPDTA    SOLUTION NMR
NUMMDL    20
AUTHOR    T.CHENG,H.LI,W.XIA,K.SZE,H.SUN
REVDAT   1   15-DEC-10 2KR7    0
JRNL        AUTH   T.CHENG,H.LI,W.XIA,K.SZE,H.SUN
JRNL        TITL   SOLUTION STRUCTURE OF HELICOBACTER PYLORI SLYD
JRNL        REF    TO BE PUBLISHED
JRNL        REFN
REMARK   2
REMARK   2 RESOLUTION. NOT APPLICABLE.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : CYANA,_AMBER, CYANA,_AMBER
REMARK   3   AUTHORS     : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA,_AMBER),
REMARK   3                 CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG,
REMARK   3                 DUKE, LUO, ... AND KOLLM (CYANA,_AMBER)
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 2KR7 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-DEC-09.
REMARK 100 THE RCSB ID CODE IS RCSB101472.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210  EXPERIMENT TYPE                : NMR
REMARK 210  TEMPERATURE           (KELVIN) : 298
REMARK 210  PH                             : 6.8
REMARK 210  IONIC STRENGTH                 : 0.1
REMARK 210  PRESSURE                       : AMBIENT
REMARK 210  SAMPLE CONTENTS                : 1-1.5 MM [U-100% 13C; U-100%
REMARK 210                                   15N] SLYD-1, 90% H2O/10% D2O; 1-
REMARK 210                                   1.5 MM [U-100% 13C; U-100% 15N]
REMARK 210                                   SLYD-2, 100% D2O
REMARK 210
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D 1H-15N HSQC; 2D 1H-13C HSQC;
REMARK 210                                   3D CBCA(CO)NH; 3D HNCACB; 3D
REMARK 210                                   HNCO; 3D HN(CA)CO; 3D C(CO)NH; 3D
REMARK 210                                   H(CCO)NH; 3D HCCH-TOCSY; 3D HCCH-
REMARK 210                                   COSY; 3D HBHA(CO)NH; 3D HNHA; 3D
REMARK 210                                   HN(CO)CA; 3D 1H-15N NOESY; 3D 1H-
REMARK 210                                   13C NOESY
REMARK 210  SPECTROMETER FIELD STRENGTH    : 600 MHZ
REMARK 210  SPECTROMETER MODEL             : AVANCE
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER
REMARK 210
REMARK 210  STRUCTURE DETERMINATION.
REMARK 210   SOFTWARE USED                 : CYANA,_AMBER
REMARK 210   METHOD USED                   : MOLECULAR DYNAMICS, SIMULATED
REMARK 210                                   ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE LOWEST 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 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 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  9 ARG A  20   NE  -  CZ  -  NH1 ANGL. DEV. =   3.0 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 LYS A  34      -72.97    -78.09
REMARK 500  1 ILE A  41      109.75    -47.86
REMARK 500  1 ASP A 106       20.41    -75.08
REMARK 500  1 ALA A 131     -176.33    -67.76
REMARK 500  1 GLU A 149       55.48    -90.94
REMARK 500  1 GLU A 150      -73.19   -138.19
REMARK 500  2 SER A   8        8.27    -69.36
REMARK 500  2 LYS A  34      -73.32   -107.87
REMARK 500  2 ILE A  41      104.58    -56.69
REMARK 500  2 ASP A  87      -36.43   -133.30
REMARK 500  2 LEU A 130       77.07   -111.31
REMARK 500  3 HIS A   4      -83.96    -74.26
REMARK 500  3 LYS A  34      -74.02    -79.48
REMARK 500  3 THR A  43      -37.79   -131.05
REMARK 500  3 GLU A  71      -56.66   -147.04
REMARK 500  3 TYR A  73       70.85     42.51
REMARK 500  3 SER A  79       52.51   -145.14
REMARK 500  3 ARG A  86       10.76    -69.73
REMARK 500  3 LYS A  96       90.48    -66.99
REMARK 500  3 ASP A 106       13.21    -69.30
REMARK 500  3 LEU A 130       76.78   -104.40
REMARK 500  4 LYS A  34      -73.58   -107.47
REMARK 500  4 ILE A  41      106.09    -50.70
REMARK 500  4 ASP A  87      -50.52   -130.63
REMARK 500  4 GLU A 149      -71.75    -84.49
REMARK 500  5 LYS A  34      -72.47    -78.59
REMARK 500  5 ILE A  41      106.74    -46.37
REMARK 500  5 ALA A  72      -70.57    -72.33
REMARK 500  5 SER A  79       79.26   -108.41
REMARK 500  5 GLU A  90       66.97     21.28
REMARK 500  5 LYS A  96       21.94    -71.81
REMARK 500  5 HIS A 128       83.77     48.46
REMARK 500  6 ILE A  41      107.69    -50.73
REMARK 500  6 ALA A  72      -67.53   -132.35
REMARK 500  6 ASP A  87      -50.36   -132.38
REMARK 500  7 GLU A   7       20.84    -75.97
REMARK 500  7 GLN A  22       93.45    -67.60
REMARK 500  7 LYS A  34      -72.17    -92.01
REMARK 500  7 ILE A  41      109.30    -47.57
REMARK 500  7 ALA A  72      -67.45   -125.51
REMARK 500  7 TYR A  80        8.03     56.55
REMARK 500  7 ALA A 131       96.49    -67.50
REMARK 500  8 GLU A   7       52.72   -102.08
REMARK 500  8 SER A   8        2.46    -69.70
REMARK 500  8 LYS A  34      -75.80   -104.27
REMARK 500  8 THR A  43      -49.61   -134.27
REMARK 500  8 ASP A  87      -50.14   -132.42
REMARK 500  9 LYS A  34      -87.97   -117.59
REMARK 500  9 ILE A  41      109.22    -54.85
REMARK 500  9 LYS A  52        0.24    -68.03
REMARK 500
REMARK 500 THIS ENTRY HAS     117 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
DBREF  2KR7 A    1   151  UNP    O25748   SLYD_HELPY       1    151
SEQRES   1 A  151  MET GLN ASN HIS ASP LEU GLU SER ILE LYS GLN ALA ALA
SEQRES   2 A  151  LEU ILE GLU TYR GLU VAL ARG GLU GLN GLY SER SER ILE
SEQRES   3 A  151  VAL LEU ASP SER ASN ILE SER LYS GLU PRO LEU GLU PHE
SEQRES   4 A  151  ILE ILE GLY THR ASN GLN ILE ILE ALA GLY LEU GLU LYS
SEQRES   5 A  151  ALA VAL LEU LYS ALA GLN ILE GLY GLU TRP GLU GLU VAL
SEQRES   6 A  151  VAL ILE ALA PRO GLU GLU ALA TYR GLY VAL TYR GLU SER
SEQRES   7 A  151  SER TYR LEU GLN GLU VAL PRO ARG ASP GLN PHE GLU GLY
SEQRES   8 A  151  ILE GLU LEU GLU LYS GLY MET SER VAL PHE GLY GLN THR
SEQRES   9 A  151  GLU ASP ASN GLN THR ILE GLN ALA ILE ILE LYS ASP PHE
SEQRES  10 A  151  SER ALA THR HIS VAL MET VAL ASP TYR ASN HIS PRO LEU
SEQRES  11 A  151  ALA GLY LYS THR LEU ALA PHE ARG PHE LYS VAL LEU GLY
SEQRES  12 A  151  PHE ARG GLU VAL SER GLU GLU GLU
HELIX    1   1 ILE A   47  LEU A   55  1                                   9
HELIX    2   2 ASP A   87  GLU A   90  5                                   4
SHEET    1   A 3 VAL A  27  SER A  30  0
SHEET    2   A 3 ALA A  12  GLU A  21 -1  N  VAL A  19   O  ASP A  29
SHEET    3   A 3 LEU A  37  ILE A  40 -1  O  PHE A  39   N  ALA A  13
SHEET    1   B 4 VAL A  27  SER A  30  0
SHEET    2   B 4 ALA A  12  GLU A  21 -1  N  VAL A  19   O  ASP A  29
SHEET    3   B 4 LEU A 135  ARG A 145 -1  O  ARG A 138   N  GLU A  18
SHEET    4   B 4 TRP A  62  ILE A  67 -1  N  GLU A  63   O  PHE A 139
SHEET    1   C 4 TYR A  80  PRO A  85  0
SHEET    2   C 4 HIS A 121  TYR A 126 -1  O  VAL A 122   N  VAL A  84
SHEET    3   C 4 GLN A 108  PHE A 117 -1  N  ASP A 116   O  MET A 123
SHEET    4   C 4 SER A  99  THR A 104 -1  N  VAL A 100   O  ALA A 112
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