› 3ieq

X-ray diffraction
2.1Å resolution

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytidine

Released:
DOI: 10.2210/pdb3ieq/pdb
PDB entry 3ieq coloured by chain, front view.
PDB entry 3ieq coloured by chain, side view.
PDB entry 3ieq coloured by chain, top view.
Source organism: Burkholderia pseudomallei
Primary publication:
Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei.
Begley DW, Hartley RC, Davies DR, Edwards TE, Leonard JT, Abendroth J, Burris CA, Bhandari J, Myler PJ, Staker BL, Stewart LJ
J Struct Funct Genomics 12 63-76 (2011)
PMID: 21359640

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-174665 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 183 amino acids
Theoretical weight: 19.49 KDa
Source organism: Burkholderia pseudomallei
Expression system: Escherichia coli
UniProt:
  • Canonical: Q3JRA0 (Residues: 1-162; Coverage: 100%)
Gene names: BURPS1710b_2511, ispF
Sequence domains: YgbB family
Structure domains: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Ligands and Environments

4 bound ligands:
Ligand C 3 x C
Ligand ZN 3 x ZN
Ligand CL 1 x CL
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: C2
Unit cell:
a: 117.27Å b: 67.7Å c: 60.34Å
α: 90° β: 96.38° γ: 90°
R-values:
R R work R free
0.175 0.172 0.225
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Molecular recognition in chemical and biological systems.
Persch et al. (2015)
8 other articles

3 mentions without citation

Combining functional and structural genomics to sample the essential Burkholderia structome.
Baugh et al. (2013)
2 more