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PDBsum entry 1jvw

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Isomerase PDB id
1jvw
Jmol
Contents
Protein chain
160 a.a. *
Waters ×271
* Residue conservation analysis
HEADER    ISOMERASE                               31-AUG-01   1JVW
TITLE     TRYPANOSOMA CRUZI MACROPHAGE INFECTIVITY POTENTIATOR (TCMIP)
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: MACROPHAGE INFECTIVITY POTENTIATOR;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: TCMIP, PEPTIDYL-PROLYL CIS-TRANS ISOMERASE,
COMPND   5 PPIASE, ROTAMASE;
COMPND   6 EC: 5.2.1.8;
COMPND   7 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: TRYPANOSOMA CRUZI;
SOURCE   3 ORGANISM_TAXID: 5693;
SOURCE   4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   5 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS    MACROPHAGE INFECTIVITY POTENTIATOR, TRYPANOSOMA CRUZI,
KEYWDS   2 CHAGAS DISEASE, X-RAY CRYSTAL STRUCTURE, ROTAMASE, ISOMERASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    P.J.B.PEREIRA,M.C.VEGA,E.GONZALEZ-REY,R.FERNANDEZ-CARAZO,
AUTHOR   2 S.MACEDO-RIBEIRO,F.X.GOMIS-RUETH,A.GONZALEZ,M.COLL
REVDAT   3   24-FEB-09 1JVW    1       VERSN
REVDAT   2   01-APR-03 1JVW    1       JRNL
REVDAT   1   05-JUN-02 1JVW    0
JRNL        AUTH   P.J.PEREIRA,M.C.VEGA,E.GONZALEZ-REY,
JRNL        AUTH 2 R.FERNANDEZ-CARAZO,S.MACEDO-RIBEIRO,F.X.GOMIS-RUTH,
JRNL        AUTH 3 A.GONZALEZ,M.COLL
JRNL        TITL   TRYPANOSOMA CRUZI MACROPHAGE INFECTIVITY
JRNL        TITL 2 POTENTIATOR HAS A ROTAMASE CORE AND A HIGHLY
JRNL        TITL 3 EXPOSED ALPHA-HELIX.
JRNL        REF    EMBO REP.                     V.   3    88 2002
JRNL        REFN                   ISSN 1469-221X
JRNL        PMID   11751578
JRNL        DOI    10.1093/EMBO-REPORTS/KVF009
REMARK   1
REMARK   2
REMARK   2 RESOLUTION.    1.70 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : SHELXL-97
REMARK   3   AUTHORS     : G.M.SHELDRICK
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 19.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   COMPLETENESS FOR RANGE        (%) : NULL
REMARK   3   CROSS-VALIDATION METHOD           : NULL
REMARK   3   FREE R VALUE TEST SET SELECTION   : RANDOM
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : 0.179
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 0.179
REMARK   3   FREE R VALUE                  (NO CUTOFF) : 0.231
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : 863
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 16999
REMARK   3
REMARK   3  FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK   3   R VALUE   (WORKING + TEST SET, F>4SIG(F)) : NULL
REMARK   3   R VALUE          (WORKING SET, F>4SIG(F)) : NULL
REMARK   3   FREE R VALUE                  (F>4SIG(F)) : NULL
REMARK   3   FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT   (F>4SIG(F)) : NULL
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (F>4SIG(F)) : NULL
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS      : 1286
REMARK   3   NUCLEIC ACID ATOMS : 0
REMARK   3   HETEROGEN ATOMS    : 0
REMARK   3   SOLVENT ATOMS      : 271
REMARK   3
REMARK   3  MODEL REFINEMENT.
REMARK   3   OCCUPANCY SUM OF NON-HYDROGEN ATOMS      : NULL
REMARK   3   OCCUPANCY SUM OF HYDROGEN ATOMS          : NULL
REMARK   3   NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL
REMARK   3   NUMBER OF LEAST-SQUARES PARAMETERS       : NULL
REMARK   3   NUMBER OF RESTRAINTS                     : NULL
REMARK   3
REMARK   3  RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK   3   BOND LENGTHS                         (A) : 0.005
REMARK   3   ANGLE DISTANCES                      (A) : 1.572
REMARK   3   SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL
REMARK   3   DISTANCES FROM RESTRAINT PLANES      (A) : NULL
REMARK   3   ZERO CHIRAL VOLUMES               (A**3) : NULL
REMARK   3   NON-ZERO CHIRAL VOLUMES           (A**3) : NULL
REMARK   3   ANTI-BUMPING DISTANCE RESTRAINTS     (A) : NULL
REMARK   3   RIGID-BOND ADP COMPONENTS         (A**2) : NULL
REMARK   3   SIMILAR ADP COMPONENTS            (A**2) : NULL
REMARK   3   APPROXIMATELY ISOTROPIC ADPS      (A**2) : NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED: NULL
REMARK   3
REMARK   3  STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER
REMARK   3   SPECIAL CASE: NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 1JVW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-01.
REMARK 100 THE RCSB ID CODE IS RCSB014244.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 20-DEC-97
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 7.5
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : EMBL/DESY, HAMBURG
REMARK 200  BEAMLINE                       : BW7B
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.885
REMARK 200  MONOCHROMATOR                  : SAGITALLY FOCUSED SI(111)
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE
REMARK 200  DETECTOR MANUFACTURER          : MARRESEARCH
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200  DATA SCALING SOFTWARE          : CCP4 (SCALA)
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 17009
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.700
REMARK 200  RESOLUTION RANGE LOW       (A) : 19.200
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 95.9
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) : 1.70
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.79
REMARK 200  COMPLETENESS FOR SHELL     (%) : 89.8
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: AMORE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 42.14
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PMSF, TRIS/HCL, PH 7.5, SMALL
REMARK 280  TUBES, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,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       17.29350
REMARK 290   SMTRY3   2  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 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     SER A    30
REMARK 465     GLY A    31
REMARK 465     ASP A    32
REMARK 465     ARG A   193
REMARK 465     GLU A   194
REMARK 465     ASP A   195
REMARK 465     MET A   196
REMARK 480
REMARK 480 ZERO OCCUPANCY ATOM
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 480   M RES C SSEQI ATOMS
REMARK 480     LYS A   79   CD    CE    NZ
REMARK 480     LYS A   87   CE    NZ
REMARK 480     LYS A  110   CD    CE    NZ
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    ALA A 145     -114.57   -122.09
REMARK 500
REMARK 500 REMARK: NULL
DBREF  1JVW A   30   196  UNP    Q09734   MIP_TRYCR       30    196
SEQRES   1 A  167  SER GLY ASP ALA ALA SER HIS GLU GLU ARG MET ASN ASN
SEQRES   2 A  167  TYR ARG LYS ARG VAL GLY ARG LEU PHE MET GLU GLN LYS
SEQRES   3 A  167  ALA ALA GLN PRO ASP ALA VAL LYS LEU PRO SER GLY LEU
SEQRES   4 A  167  VAL PHE GLN ARG ILE ALA ARG GLY SER GLY LYS ARG ALA
SEQRES   5 A  167  PRO ALA ILE ASP ASP LYS CYS GLU VAL HIS TYR THR GLY
SEQRES   6 A  167  ARG LEU ARG ASP GLY THR VAL PHE ASP SER SER ARG GLU
SEQRES   7 A  167  ARG GLY LYS PRO THR THR PHE ARG PRO ASN GLU VAL ILE
SEQRES   8 A  167  LYS GLY TRP THR GLU ALA LEU GLN LEU MET ARG GLU GLY
SEQRES   9 A  167  ASP ARG TRP ARG LEU PHE ILE PRO TYR ASP LEU ALA TYR
SEQRES  10 A  167  GLY VAL THR GLY GLY GLY GLY MET ILE PRO PRO TYR SER
SEQRES  11 A  167  PRO LEU GLU PHE ASP VAL GLU LEU ILE SER ILE LYS ASP
SEQRES  12 A  167  GLY GLY LYS GLY ARG THR ALA GLU GLU VAL ASP GLU ILE
SEQRES  13 A  167  LEU ARG LYS ALA GLU GLU ASP ARG GLU ASP MET
FORMUL   2  HOH   *271(H2 O)
HELIX    1   1 SER A   35  GLN A   58  1                                  24
HELIX    2   2 SER A  105  GLY A  109  1                                   5
HELIX    3   3 ARG A  115  VAL A  119  5                                   5
HELIX    4   4 ILE A  120  GLN A  128  1                                   9
HELIX    5   5 PRO A  141  ALA A  145  5                                   5
HELIX    6   6 ASP A  172  GLY A  174  5                                   3
HELIX    7   7 THR A  178  ASP A  192  1                                  15
SHEET    1   A 6 ALA A  61  LYS A  63  0
SHEET    2   A 6 VAL A  69  ALA A  74 -1  O  PHE A  70   N  VAL A  62
SHEET    3   A 6 ARG A 135  ILE A 140 -1  O  PHE A 139   N  VAL A  69
SHEET    4   A 6 LEU A 161  ILE A 170 -1  O  VAL A 165   N  TRP A 136
SHEET    5   A 6 CYS A  88  ARG A  95 -1  N  ARG A  95   O  GLU A 162
SHEET    6   A 6 VAL A 101  SER A 104 -1  O  ASP A 103   N  GLY A  94
SHEET    1   B 6 ALA A  61  LYS A  63  0
SHEET    2   B 6 VAL A  69  ALA A  74 -1  O  PHE A  70   N  VAL A  62
SHEET    3   B 6 ARG A 135  ILE A 140 -1  O  PHE A 139   N  VAL A  69
SHEET    4   B 6 LEU A 161  ILE A 170 -1  O  VAL A 165   N  TRP A 136
SHEET    5   B 6 CYS A  88  ARG A  95 -1  N  ARG A  95   O  GLU A 162
SHEET    6   B 6 THR A 112  PHE A 114 -1  O  PHE A 114   N  CYS A  88
CRYST1   46.034   34.587   50.412  90.00  91.57  90.00 P 1 21 1      2
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      0.021723  0.000000  0.000595        0.00000
SCALE2      0.000000  0.028913  0.000000        0.00000
SCALE3      0.000000  0.000000  0.019844        0.00000
      
PROCHECK
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 References