› 5y5i

X-ray diffraction
2.1Å resolution

Time-resolved SFX structure of cytochrome P450nor: 20 ms after photo-irradiation of caged NO in the presence of NADH (NO-bound state), light data

Released:
DOI: 10.2210/pdb5y5i/pdb
PDB entry 5y5i coloured by chain, front view.
PDB entry 5y5i coloured by chain, side view.
PDB entry 5y5i coloured by chain, top view.
Source organism: Fusarium oxysporum
Primary publication:
Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Tosha T, Nomura T, Nishida T, Saeki N, Okubayashi K, Yamagiwa R, Sugahara M, Nakane T, Yamashita K, Hirata K, Ueno G, Kimura T, Hisano T, Muramoto K, Sawai H, Takeda H, Mizohata E, Yamashita A, Kanematsu Y, Takano Y, Nango E, Tanaka R, Nureki O, Shoji O, Ikemoto Y, Murakami H, Owada S, Tono K, Yabashi M, Yamamoto M, Ago H, Iwata S, Sugimoto H, Shiro Y, Kubo M
Nat Commun 8 1585 (2017)
PMID: 29147002

Function and Biology Details

Reaction catalysed: 
Nitrous oxide + NAD(P)(+) + H(2)O = 2 nitric oxide + NAD(P)H
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149924 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
NADP nitrous oxide-forming nitric oxide reductase Chains: A, B
Molecule details ›
Chains: A, B
Length: 403 amino acids
Theoretical weight: 44.42 KDa
Source organism: Fusarium oxysporum
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P23295 (Residues: 1-403; Coverage: 100%)
Gene names: CYP55, CYP55A1
Sequence domains: Cytochrome P450
Structure domains: Cytochrome P450

Ligands and Environments


Cofactor: Ligand HEM 2 x HEM
2 bound ligands:
Ligand NO 2 x NO
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SACLA BEAMLINE BL3
Spacegroup: P21
Unit cell:
a: 54.6Å b: 102.3Å c: 73.7Å
α: 90° β: 92.6° γ: 90°
R-values:
R R work R free
0.15 0.148 0.196
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

11 review citations

Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics.
Srivastava et al. (2018)
10 more

1 mention without citation

Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Tosha et al. (2017)