› 6vcf

X-ray diffraction
2.69Å resolution

Crystal structure of Nitrosotalea devanaterra carotenoid cleavage dioxygenase, iron form

Released:
DOI: 10.2210/pdb6vcf/pdb
PDB entry 6vcf coloured by chain, front view.
PDB entry 6vcf coloured by chain, side view.
PDB entry 6vcf coloured by chain, top view.
Source organism: Candidatus Nitrosotalea devanaterra
Primary publication:
Structural basis for carotenoid cleavage by an archaeal carotenoid dioxygenase.
Daruwalla A, Zhang J, Lee HJ, Khadka N, Farquhar ER, Shi W, von Lintig J, Kiser PD
Proc Natl Acad Sci U S A 117 19914-19925 (2020)
PMID: 32747548

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-102894 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Putative dioxygenase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 472 amino acids
Theoretical weight: 53.88 KDa
Source organism: Candidatus Nitrosotalea devanaterra
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A128A3G4 (Residues: 1-472; Coverage: 100%)
Gene name: NDEV_1113
Sequence domains: Retinal pigment epithelial membrane protein

Ligands and Environments

4 bound ligands:
Ligand FE2 6 x FE2
Ligand CL 1 x CL
Ligand NA 2 x NA
Ligand BCT 2 x BCT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS-II BEAMLINE 17-ID-2
Spacegroup: P61
Unit cell:
a: 107.267Å b: 107.267Å c: 491.109Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.253 0.252 0.271
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Pathways and disease-causing alterations in visual chromophore production for vertebrate vision.
Kiser et al. (2021)
2 more

1 mention without citation

Structural and Functional Analysis of Nonheme Iron Enzymes BCMO-1 and BCMO-2 from Caenorhabditis elegans.
Pan et al. (2022)