› 4qcd

Hybrid

Neutron crystal structure of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin IXalpha at room temperature.

Released:
DOI: 10.2210/pdb4qcd/pdb
PDB entry 4qcd coloured by chain, front view.
PDB entry 4qcd coloured by chain, side view.
PDB entry 4qcd coloured by chain, top view.
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
Primary publication:
Insights into the Proton Transfer Mechanism of a Bilin Reductase PcyA Following Neutron Crystallography.
Unno M, Ishikawa-Suto K, Kusaka K, Tamada T, Hagiwara Y, Sugishima M, Wada K, Yamada T, Tomoyori K, Hosoya T, Tanaka I, Niimura N, Kuroki R, Inaka K, Ishihara M, Fukuyama K
J Am Chem Soc 137 5452-60 (2015)
PMID: 25872660

Function and Biology Details

Reaction catalysed: 
(3Z)-phycocyanobilin + 4 oxidized ferredoxin = biliverdin IX-alpha + 4 reduced ferredoxin
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176303 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phycocyanobilin:ferredoxin oxidoreductase Chain: A
Molecule details ›
Chain: A
Length: 248 amino acids
Theoretical weight: 28.16 KDa
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
Expression system: Escherichia coli
UniProt:
  • Canonical: Q55891 (Residues: 1-248; Coverage: 100%)
Gene names: pcyA, slr0116
Sequence domains: Ferredoxin-dependent bilin reductase
Structure domains: oxygen-dependent coproporphyrinogen oxidase

Ligands and Environments

2 bound ligands:
Ligand BLA 1 x BLA
Ligand D3O 1 x D3O
No modified residues

Experiments and Validation Details

Experimental Method: Neutron Diffraction, X-ray diffraction
X-ray source: J-PARC MLF BEAMLINE BL-03, PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: P21212
Unit cell:
a: 71.107Å b: 97.278Å c: 43.174Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.173 0.143 0.227
Expression system: Escherichia coli

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Citations

1 review citation

The use of neutron scattering to determine the functional structure of glycoside hydrolase.
Nakamura et al. (2016)
11 other articles

4 mentions without citation

Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition.
Liebschner et al. (2018)
3 more