› 3p13

X-ray diffraction
2.35Å resolution

Complex Structure of D-ribose Pyranase Sa240 with D-ribose

Released:
DOI: 10.2210/pdb3p13/pdb
PDB entry 3p13 coloured by chain, front view.
PDB entry 3p13 coloured by chain, side view.
PDB entry 3p13 coloured by chain, top view.
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
Primary publication:
Crystal structure of Sa240: a ribose pyranase homolog with partial active site from Staphylococcus aureus.
Wang L, Wu M, Zang J
J Struct Biol 174 413-9 (2011)
PMID: 21276853

Function and Biology Details

Reaction catalysed: 
Beta-D-ribopyranose = beta-D-ribofuranose
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-173517 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-ribose pyranase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 144 amino acids
Theoretical weight: 16.44 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
Expression system: Escherichia coli
UniProt:
  • Canonical: Q2G1A5 (Residues: 1-134; Coverage: 100%)
Gene names: SAOUHSC_00240, rbsD
Sequence domains: RbsD / FucU transport protein family
Structure domains: RbsD-like domain

Ligands and Environments

1 bound ligand:
Ligand RIP 4 x RIP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P64
Unit cell:
a: 124.27Å b: 124.27Å c: 86.21Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.215 0.213 0.25
Expression system: Escherichia coli

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Citations

29 mentions without citation

The use of genomics, proteomics, and metabolomics in identifying biomarkers of male infertility.
Kovac et al. (2013)
28 more