3KCL

Room temperature neutron structure of D-Xylose Isomerase in complex with two Cd2+ cations and d12-D-alpha-glucose in the ring form (refined jointly with X-ray structure 3KBM)

Structural Biology Knowledgebase: 3KCL SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION, NEUTRON DIFFRACTION
  • Resolution: --
  • R-Value Free: 0.194
  • R-Value Work: 0.173

Currently 3KCL does not have a wwPDB validation report.


Literature

Macromolecules
Sequence Display for 3KCL

Classification: ISOMERASE

Total Structure Weight: 43688.71

Macromolecule Entities
Molecule Chains Length Organism Details
Xylose isomerase A 388 Streptomyces rubiginosus EC#: 5.3.1.5 IUBMB
Gene Name(s): xylA

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GLC
Query on GLC

A ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

A CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DOD
Query on DOD

A DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION, NEUTRON DIFFRACTION
  • Resolution: -- Å
  • R-Value Free: 0.194
  • R-Value Work: 0.173
  • Space Group: I 2 2 2

Unit Cell:

Length (Å) Angle (°)
a = 94.20 α = 90.00
b = 99.43 β = 90.00
c = 102.99 γ = 90.00

Structure Validation

Currently 3KCL does not have a validation report.



Entry History

Deposition Data

  • Deposited Date: 2009-10-21
  • Released Date: 2010-06-16
  • Deposition author(s): Kovalevsky, A.Y., Langan, P.

Revision History

  • 2012-03-07
    Type: Citation | Details: Citation update
  • 2011-07-27
    Type: Data collection | Details: hybrid method
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4