1CLK

CRYSTAL STRUCTURE OF STREPTOMYCES DIASTATICUS NO.7 STRAIN M1033 XYLOSE ISOMERASE AT 1.9 A RESOLUTION WITH PSEUDO-I222 SPACE GROUP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of xylose isomerase from Streptomyces diastaticus no. 7 strain M1033 at 1.85 A resolution.

Zhu, X.Teng, M.Niu, L.Xu, C.Wang, Y.

(2000) Acta Crystallogr.,Sect.D 56: 129-136

  • Primary Citation of Related Structures:  1QT1

  • PubMed Abstract: 
  • The structure of xylose isomerase (XyI) from Streptomyces diastaticus No. 7 strain M1033 (SDXyI) has been refined at 1.85 A resolution to conventional and free R factors of 0.166 and 0.219, respectively. SDXyI was crystallized in space group P2(1)2(1 ...

    The structure of xylose isomerase (XyI) from Streptomyces diastaticus No. 7 strain M1033 (SDXyI) has been refined at 1.85 A resolution to conventional and free R factors of 0.166 and 0.219, respectively. SDXyI was crystallized in space group P2(1)2(1)2, with unit-cell parameters a = 87.976, b = 98.836, c = 93.927 A. One dimer of the tetrametric molecule is found in each asymmetric unit. Each monomer consists of two domains: a large N-terminal domain (residues 1-320), containing a parallel eight-stranded alpha/beta barrel, and a small C-terminal loop (residues 321-387), containing five helices linked by random coil. The four monomers are essentially identical in the tetramer, possessing non-crystallographic 222 symmetry with one twofold axis essentially coincident with the crystallographic twofold axis in the space group P2(1)2(1)2, which may explain why the diffraction pattern has strong pseudo-I222 symmetry even at medium resolution. The crystal structures of XyIs from different bacterial strains, especially from Streptomyces, are similar. The alpha2 helix of the alpha/beta barrel has a different position in the structures of different XyIs. The conformation of C-terminal fragment 357-364 in the SDXyI structure has a small number of differences to that of other XyIs. Two Co(2+) ions rather than Mg(2+) ions exist in the active site of the SDXyI structure; SDXyI seems to prefer to bind Co(2+) ions rather than Mg(2+) ions.


    Related Citations: 
    • Growth of Single Crystals and Preliminary Analysis of Glucose Isomerase From Streptomyces M1033
      Zhang, G.Y.,Niu, L.W.,Huang, W.Z.,Wang, C.,Liu, J.,Cui, Y.,Liu, X.A.,Wang, Y.Z.,Xu, X.,Liang, D.C.
      (1991) Chin.Sci.Bull. 36: 1646
    • Crystal Structure of Streptomyces diastaticus No.7 Strain M1033 Xylose Isomerase
      Zhu, X.,Gong, W.,Niu, L.,Teng, M.,Xu, C.,Wu, C.,Cui, T.,Wang, Y.,Wang, C.
      (1996) SCI.CHINA, SER.C: LIFE SCI. 39: 636


    Organizational Affiliation

    Department of Molecular Biology, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
XYLOSE ISOMERASE
A
387Streptomyces diastaticusGene Names: xylA
EC: 5.3.1.5
Find proteins for P50910 (Streptomyces diastaticus)
Go to UniProtKB:  P50910
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.186 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 98.836α = 90.00
b = 93.927β = 90.00
c = 87.976γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-GENdata scaling
X-GENdata reduction
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-03
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description