2GLK

High-resolution study of D-Xylose isomerase, 0.94A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.94 Å
  • R-Value Free: 0.128 
  • R-Value Work: 0.115 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Locating active-site hydrogen atoms in D-xylose isomerase: Time-of-flight neutron diffraction.

Katz, A.K.Li, X.Carrell, H.L.Hanson, B.L.Langan, P.Coates, L.Schoenborn, B.P.Glusker, J.P.Bunick, G.J.

(2006) Proc.Natl.Acad.Sci.Usa 103: 8342-8347

  • DOI: 10.1073/pnas.0602598103
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Time-of-flight neutron diffraction has been used to locate hydrogen atoms that define the ionization states of amino acids in crystals of D-xylose isomerase. This enzyme, from Streptomyces rubiginosus, is one of the largest enzymes studied to date at ...

    Time-of-flight neutron diffraction has been used to locate hydrogen atoms that define the ionization states of amino acids in crystals of D-xylose isomerase. This enzyme, from Streptomyces rubiginosus, is one of the largest enzymes studied to date at high resolution (1.8 A) by this method. We have determined the position and orientation of a metal ion-bound water molecule that is located in the active site of the enzyme; this water has been thought to be involved in the isomerization step in which D-xylose is converted to D-xylulose or D-glucose to D-fructose. It is shown to be water (rather than a hydroxyl group) under the conditions of measurement (pH 8.0). Our analyses also reveal that one lysine probably has an -NH(2)-terminal group (rather than NH(3)(+)). The ionization state of each histidine residue also was determined. High-resolution x-ray studies (at 0.94 A) indicate disorder in some side chains when a truncated substrate is bound and suggest how some side chains might move during catalysis. This combination of time-of-flight neutron diffraction and x-ray diffraction can contribute greatly to the elucidation of enzyme mechanisms.


    Organizational Affiliation

    Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xylose isomerase
A
388Streptomyces rubiginosusMutation(s): 0 
Gene Names: xylA
EC: 5.3.1.5
Find proteins for P24300 (Streptomyces rubiginosus)
Go to UniProtKB:  P24300
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.94 Å
  • R-Value Free: 0.128 
  • R-Value Work: 0.115 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 92.712α = 90.00
b = 97.935β = 90.00
c = 101.867γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
HKL-2000data scaling
X-GENdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-16
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description