› 5d9d

X-ray diffraction
1.7Å resolution

Luciferin-regenerating enzyme solved by SAD using synchrotron radiation at room temperature

Released:
DOI: 10.2210/pdb5d9d/pdb
PDB entry 5d9d coloured by chain, front view.
PDB entry 5d9d coloured by chain, side view.
PDB entry 5d9d coloured by chain, top view.
Source organism: Photinus pyralis
Primary publication:
An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Yamashita K, Pan D, Okuda T, Sugahara M, Kodan A, Yamaguchi T, Murai T, Gomi K, Kajiyama N, Mizohata E, Suzuki M, Nango E, Tono K, Joti Y, Kameshima T, Park J, Song C, Hatsui T, Yabashi M, Iwata S, Kato H, Ago H, Yamamoto M, Nakatsu T
Sci Rep 5 14017 (2015)
PMID: 26360462

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188283 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
SMP-30/Gluconolactonase/LRE-like region domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 311 amino acids
Theoretical weight: 34.2 KDa
Source organism: Photinus pyralis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q95YI4 (Residues: 1-308; Coverage: 100%)
Sequence domains: SMP-30/Gluconolactonase/LRE-like region
Structure domains: TolB, C-terminal domain

Ligands and Environments

3 bound ligands:
Ligand MG 1 x MG
Ligand HG 3 x HG
Ligand MPD 1 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B2
Spacegroup: P212121
Unit cell:
a: 48.107Å b: 77.177Å c: 84.916Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.146 0.144 0.178
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

A Bright Future for Serial Femtosecond Crystallography with XFELs.
Johansson et al. (2017)
5 more

1 mention without citation

An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Yamashita et al. (2015)