› 5iwx

X-ray diffraction
1.99Å resolution

Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Bacillus subtitis

Released:
DOI: 10.2210/pdb5iwx/pdb
PDB entry 5iwx coloured by chain, front view.
PDB entry 5iwx coloured by chain, side view.
PDB entry 5iwx coloured by chain, top view.
Source organism: Bacillus subtilis subsp. subtilis str. 168
Primary publication:
Crystal structure of IspF from Bacillus subtilis and absence of protein complex assembly amongst IspD/IspE/IspF enzymes in the MEP pathway.
Liu Z, Jin Y, Liu W, Tao Y, Wang G
Biosci Rep 38 (2018)
PMID: 29335298

Function and Biology Details

Reaction catalysed: 
2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170386 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 158 amino acids
Theoretical weight: 17.15 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
Expression system: Escherichia coli
UniProt:
  • Canonical: Q06756 (Residues: 1-158; Coverage: 100%)
Gene names: BSU00910, ispF, yacN
Sequence domains: YgbB family

Ligands and Environments

1 bound ligand:
Ligand MG 6 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P21
Unit cell:
a: 56.964Å b: 89.295Å c: 84.708Å
α: 90° β: 100.85° γ: 90°
R-values:
R R work R free
0.184 0.181 0.231
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Positioning Bacillus subtilis as terpenoid cell factory.
Pramastya et al. (2021)
1 more

1 mention without citation

Crystal structure of IspF from Bacillus subtilis and absence of protein complex assembly amongst IspD/IspE/IspF enzymes in the MEP pathway.
Liu et al. (2018)