› 3l0s

X-ray diffraction
2Å resolution

Crystal structures of Zinc, Cobalt and Iron containing Adenylate kinase from Gram-negative bacteria Desulfovibrio gigas

Released:
DOI: 10.2210/pdb3l0s/pdb
PDB entry 3l0s coloured by chain, front view.
PDB entry 3l0s coloured by chain, side view.
PDB entry 3l0s coloured by chain, top view.
Source organism: Megalodesulfovibrio gigas
Primary publication:
Crystal structure of the zinc-, cobalt-, and iron-containing adenylate kinase from Desulfovibrio gigas: a novel metal-containing adenylate kinase from Gram-negative bacteria.
Mukhopadhyay A, Kladova AV, Bursakov SA, Gavel OY, Calvete JJ, Shnyrov VL, Moura I, Moura JJ, Romão MJ, Trincão J
J Biol Inorg Chem 16 51-61 (2011)
PMID: 20821240

Function and Biology Details

Reaction catalysed: 
ATP + AMP = 2 ADP
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111779 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Adenylate kinase Chains: A, C
Molecule details ›
Chains: A, C
Length: 223 amino acids
Theoretical weight: 24.54 KDa
Source organism: Megalodesulfovibrio gigas
Expression system: Escherichia coli
UniProt:
  • Canonical: C7U112 (Residues: 1-223; Coverage: 100%)
Gene names: adk, ak
Sequence domains: Adenylate kinase
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

2 bound ligands:
Ligand CO 2 x CO
Ligand TAR 2 x TAR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: C2
Unit cell:
a: 131.43Å b: 39.49Å c: 94.2Å
α: 90° β: 109.31° γ: 90°
R-values:
R R work R free
0.193 0.19 0.254
Expression system: Escherichia coli

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Citations

1 review citation

Normal Mode Analysis as a Routine Part of a Structural Investigation.
Bauer et al. (2019)
5 other articles