› 4qdw

Hybrid

Joint X-ray and neutron structure of Streptomyces rubiginosus D-xylose isomerase in complex with two Ni2+ ions and linear L-arabinose

Released:
DOI: 10.2210/pdb4qdw/pdb
PDB entry 4qdw coloured by chain, front view.
PDB entry 4qdw coloured by chain, side view.
PDB entry 4qdw coloured by chain, top view.
Source organism: Streptomyces rubiginosus
Primary publication:
L-Arabinose binding, isomerization, and epimerization by D-xylose isomerase: X-ray/neutron crystallographic and molecular simulation study.
Langan P, Sangha AK, Wymore T, Parks JM, Yang ZK, Hanson BL, Fisher Z, Mason SA, Blakeley MP, Forsyth VT, Glusker JP, Carrell HL, Smith JC, Keen DA, Graham DE, Kovalevsky A
Structure 22 1287-1300 (2014)
PMID: 25132082

Function and Biology Details

Reaction catalysed: 
Alpha-D-xylopyranose = alpha-D-xylufuranose
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-540717 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Xylose isomerase Chain: A
Molecule details ›
Chain: A
Length: 388 amino acids
Theoretical weight: 43.28 KDa
Source organism: Streptomyces rubiginosus
UniProt:
  • Canonical: P24300 (Residues: 1-388; Coverage: 100%)
Gene name: xylA
Sequence domains: Xylose isomerase-like TIM barrel
Structure domains: Divalent-metal-dependent TIM barrel enzymes

Ligands and Environments

3 bound ligands:
Ligand NI 3 x NI
Ligand LAI 1 x LAI
Ligand DOD 259 x DOD
No modified residues

Experiments and Validation Details

Experimental Method: Neutron Diffraction, X-ray diffraction
X-ray source: RIGAKU MICROMAX-007 HF, null
Spacegroup: I222
Unit cell:
a: 94.19Å b: 99.67Å c: 102.94Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.166 not available 0.179

Quick links

Citations

2 review citations

Neutron protein crystallography: A complementary tool for locating hydrogens in proteins.
O'Dell et al. (2016)
1 more

4 mentions without citation

Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition.
Liebschner et al. (2018)
3 more