› 3f0f

X-ray diffraction
2.09Å resolution

Co-crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with hydrolyzed CDP

Released:
DOI: 10.2210/pdb3f0f/pdb
PDB entry 3f0f coloured by chain, front view.
PDB entry 3f0f coloured by chain, side view.
PDB entry 3f0f coloured by chain, top view.
Source organism: Burkholderia pseudomallei
Primary publication:
Combining functional and structural genomics to sample the essential Burkholderia structome.
Baugh L, Gallagher LA, Patrapuvich R, Clifton MC, Gardberg AS, Edwards TE, Armour B, Begley DW, Dieterich SH, Dranow DM, Abendroth J, Fairman JW, Fox D, Staker BL, Phan I, Gillespie A, Choi R, Nakazawa-Hewitt S, Nguyen MT, Napuli A, Barrett L, Buchko GW, Stacy R, Myler PJ, Stewart LJ, Manoil C, Van Voorhis WC
PLoS One 8 e53851 (2013)
PMID: 23382856

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 GOL 1 x GOL
Ligand MG 1 x MG
Ligand ZN 3 x ZN
Ligand C5P 1 x C5P
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 53.078Å b: 66.457Å c: 131.465Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.197 0.246
Expression system: Escherichia coli

Quick links

Citations

11 review citations

Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product.
Dailey et al. (2017)
10 more

3 mentions without citation

The Seattle Structural Genomics Center for Infectious Disease (SSGCID).
Myler et al. (2009)
2 more