› 3qys

X-ray diffraction
1.85Å resolution

Room Temperature X-ray Structure of D-Xylose Isomerase in complex with 0.6Ni2+ cation bound in M2 metal binding site at pH=5.8

Released:
DOI: 10.2210/pdb3qys/pdb
PDB entry 3qys coloured by chain, front view.
PDB entry 3qys coloured by chain, side view.
PDB entry 3qys coloured by chain, top view.
Source organism: Streptomyces rubiginosus
Primary publication:
Identification of the elusive hydronium ion exchanging roles with a proton in an enzyme at lower pH values.
Kovalevsky AY, Hanson BL, Mason SA, Yoshida T, Fisher SZ, Mustyakimov M, Forsyth VT, Blakeley MP, Keen DA, Langan P
Angew Chem Int Ed Engl 50 7520-3 (2011)
PMID: 21604345

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

1 bound ligand:
Ligand NI 1 x NI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E DW
Spacegroup: I222
Unit cell:
a: 94.9Å b: 99.63Å c: 102.84Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.173 0.171 0.218

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Citations

5 review citations

Regulation of Amino Acid Transport in Saccharomyces cerevisiae.
Bianchi et al. (2019)
4 more