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: 1.90 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 D Biol Crystallogr 56: 129-136

  • DOI: 10.1107/s0907444999015097
  • Primary Citation of Related Structures:  
    1QT1, 1CLK

  • 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)2, with unit-cell parameters a = 87 ...

    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: 
    • 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 C Life Sci 39: 636
    • 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

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
XYLOSE ISOMERASEA387Streptomyces diastaticusMutation(s): 0 
Gene Names: xylA
EC: 5.3.1.5
UniProt
Find proteins for P50910 (Streptomyces diastaticus)
Explore P50910 
Go to UniProtKB:  P50910
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO

Download Ideal Coordinates CCD File 
C [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.186 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.836α = 90
b = 93.927β = 90
c = 87.976γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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