› 4y8v

X-ray diffraction
2.1Å resolution

Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme A synthetase 1 in complex with ADP and additional ADP bound to phosphate binding site

Released:
DOI: 10.2210/pdb4y8v/pdb
PDB entry 4y8v coloured by chain, front view.
PDB entry 4y8v coloured by chain, side view.
PDB entry 4y8v coloured by chain, top view.
Source organism: Candidatus Korarchaeum cryptofilum OPF8
Primary publication:
Structure of NDP-forming Acetyl-CoA synthetase ACD1 reveals a large rearrangement for phosphoryl transfer.
Weiße RH, Faust A, Schmidt M, Schönheit P, Scheidig AJ
Proc Natl Acad Sci U S A 113 E519-28 (2016)
PMID: 26787904

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109326 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
CoA-binding domain-containing protein Chains: A, C
Molecule details ›
Chains: A, C
Length: 464 amino acids
Theoretical weight: 49.35 KDa
Source organism: Candidatus Korarchaeum cryptofilum OPF8
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B1L3C9 (Residues: 1-464; Coverage: 100%)
Gene name: Kcr_0198
Sequence domains:
Structure domains:
ATP-grasp domain-containing protein Chains: B, D
Molecule details ›
Chains: B, D
Length: 230 amino acids
Theoretical weight: 25.68 KDa
Source organism: Candidatus Korarchaeum cryptofilum OPF8
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B1L7P8 (Residues: 1-230; Coverage: 100%)
Gene name: Kcr_0115
Sequence domains: ATP-grasp domain
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand ADP 4 x ADP
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P212121
Unit cell:
a: 106.47Å b: 110.99Å c: 126.72Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.184 0.226
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

The many ways that nature has exploited the unusual structural and chemical properties of phosphohistidine for use in proteins.
Kalagiri et al. (2021)
1 more

1 mention without citation

Structure of NDP-forming Acetyl-CoA synthetase ACD1 reveals a large rearrangement for phosphoryl transfer.
Weiße et al. (2016)