› 6oby

X-ray diffraction
2.87Å resolution

The nucleotide-binding protein AF_226 in complex with ADP from Archaeoglobus fulgidus with Co found by PIXE. Based on 3KB1.

Released:
DOI: 10.2210/pdb6oby/pdb
PDB entry 6oby coloured by chain, front view.
PDB entry 6oby coloured by chain, side view.
PDB entry 6oby coloured by chain, top view.
Source organism: Archaeoglobus fulgidus
Primary publication:
High-Throughput PIXE as an Essential Quantitative Assay for Accurate Metalloprotein Structural Analysis: Development and Application.
Grime GW, Zeldin OB, Snell ME, Lowe ED, Hunt JF, Montelione GT, Tong L, Snell EH, Garman EF
J Am Chem Soc 142 185-197 (2020)
PMID: 31794207

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127928 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Iron-sulfur cluster carrier protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 262 amino acids
Theoretical weight: 29.46 KDa
Source organism: Archaeoglobus fulgidus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O28015 (Residues: 1-254; Coverage: 100%)
Gene name: AF_2269
Sequence domains: NUBPL iron-transfer P-loop NTPase

Ligands and Environments

2 bound ligands:
Ligand ADP 2 x ADP
Ligand CO 1 x CO
1 modified residue:
Ligand MSE 14 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4C
Spacegroup: P21
Unit cell:
a: 51.44Å b: 67.682Å c: 79.403Å
α: 90° β: 90.09° γ: 90°
R-values:
R R work R free
0.22 0.217 0.284
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Learning to Identify Physiological and Adventitious Metal-Binding Sites in the Three-Dimensional Structures of Proteins by Following the Hints of a Deep Neural Network.
Laveglia et al. (2022)
1 more