6icm

X-ray diffraction
2.96Å resolution

Pseudomonas putida CBB5 NdmA with ferredoxin domain of NdmD

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
PDBe Complex ID:
PDB-CPX-124961 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Methylxanthine N1-demethylase NdmA Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 369 amino acids
Theoretical weight: 42.38 KDa
Source organism: Pseudomonas putida
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: H9N289 (Residues: 1-351; Coverage: 100%)
Gene name: ndmA
Sequence domains:
Oxidoreductase NdmD Chain: D
Molecule details ›
Chain: D
Length: 87 amino acids
Theoretical weight: 9.66 KDa
Source organism: Pseudomonas putida
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: H9N291 (Residues: 502-588; Coverage: 15%)
Gene name: ndmD
Sequence domains: 2Fe-2S iron-sulfur cluster binding domain

Ligands and Environments

3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P6122
Unit cell:
a: 118.265Å b: 118.265Å c: 455.692Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.206 0.204 0.261
Expression system: Escherichia coli BL21(DE3)