› 2pmb

X-ray diffraction
1.99Å resolution

Crystal structure of predicted nucleotide-binding protein from Vibrio cholerae

Released:
DOI: 10.2210/pdb2pmb/pdb
PDB entry 2pmb coloured by chain, front view.
PDB entry 2pmb coloured by chain, side view.
PDB entry 2pmb coloured by chain, top view.
Source organism: Vibrio cholerae
Entry authors: Patskovsky Y, Zhan C, Shi W, Toro R, Sauder JM, Gilmore J, Iizuka M, Maletic M, Gheyi T, Wasserman SR, Smith D, Burley SK, Almo SC, New York SGX Research Center for Structural Genomics (NYSGXRC)

Function and Biology Details

Reaction catalysed: 
AMP + H(2)O = D-ribose 5-phosphate + adenine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192094 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
AMP nucleosidase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 462 amino acids
Theoretical weight: 52.57 KDa
Source organism: Vibrio cholerae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9KTK3 (Residues: 7-457; Coverage: 99%)
Gene name: VC_0899
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand PO4 12 x PO4
Ligand GOL 2 x GOL
1 modified residue:
Ligand MSE 72 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P21
Unit cell:
a: 58.802Å b: 178.222Å c: 89.513Å
α: 90° β: 103.78° γ: 90°
R-values:
R R work R free
0.21 0.208 0.266
Expression system: Escherichia coli BL21(DE3)

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