› 4duo

X-ray diffraction
2Å resolution

Room-temperature X-ray structure of D-Xylose Isomerase in complex with 2Mg2+ ions and xylitol at pH 7.7

Released:
DOI: 10.2210/pdb4duo/pdb
PDB entry 4duo coloured by chain, front view.
PDB entry 4duo coloured by chain, side view.
PDB entry 4duo coloured by chain, top view.
Source organism: Streptomyces rubiginosus
Primary publication:
Inhibition of D-xylose isomerase by polyols: atomic details by joint X-ray/neutron crystallography.
Kovalevsky A, Hanson BL, Mason SA, Forsyth VT, Fisher Z, Mustyakimov M, Blakeley MP, Keen DA, Langan P
Acta Crystallogr D Biol Crystallogr 68 1201-6 (2012)
PMID: 22948921

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-150204 (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

2 bound ligands:
Ligand MG 2 x MG
Ligand XYL 1 x XYL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E DW
Spacegroup: I222
Unit cell:
a: 93.79Å b: 99.62Å c: 102.83Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.148 0.141 0.2

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Citations

1 review citation

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

3 mentions without citation

Invariant gly residue is important for α-defensin folding, dimerization, and function: a case study of the human neutrophil α-defensin HNP1.
Zhao et al. (2012)
2 more