› 3kbm

X-ray diffraction
2Å resolution

Room Temperature X-ray structure of D-Xylose Isomerase complexed with 2Cd(2+) co-factors and d12-D-alpha-glucose in the cyclic form

Released:
DOI: 10.2210/pdb3kbm/pdb
PDB entry 3kbm coloured by chain, front view.
PDB entry 3kbm coloured by chain, side view.
PDB entry 3kbm coloured by chain, top view.
Source organism: Streptomyces rubiginosus
Primary publication:
Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.
Kovalevsky AY, Hanson L, Fisher SZ, Mustyakimov M, Mason SA, Forsyth VT, Blakeley MP, Keen DA, Wagner T, Carrell HL, Katz AK, Glusker JP, Langan P
Structure 18 688-99 (2010)
PMID: 20541506

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
Expression system: Not provided
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 CD 2 x CD
Ligand GLC 1 x GLC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E DW
Spacegroup: I222
Unit cell:
a: 94.196Å b: 99.43Å c: 102.986Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.176 0.211
Expression system: Not provided

Quick links

Citations

5 review citations

Industrial use of immobilized enzymes.
DiCosimo et al. (2013)
4 more

2 mentions without citation

Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.
Kovalevsky et al. (2010)
1 more