› 6nmo

X-ray diffraction
1.45Å resolution

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand SR-4

Released:
DOI: 10.2210/pdb6nmo/pdb
PDB entry 6nmo coloured by chain, front view.
PDB entry 6nmo coloured by chain, side view.
PDB entry 6nmo coloured by chain, top view.
Source organism: Burkholderia pseudomallei 1710b
Entry author: Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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: 163 amino acids
Theoretical weight: 17.28 KDa
Source organism: Burkholderia pseudomallei 1710b
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q3JRA0 (Residues: 1-162; Coverage: 100%)
Gene names: BURPS1710b_2511, ispF
Sequence domains: YgbB family

Ligands and Environments

5 bound ligands:
Ligand ZN 3 x ZN
Ligand DMS 1 x DMS
Ligand MLI 3 x MLI
Ligand EDO 3 x EDO
Ligand QMS 1 x QMS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: C2
Unit cell:
a: 117.08Å b: 67.6Å c: 60.81Å
α: 90° β: 96.48° γ: 90°
R-values:
R R work R free
0.127 0.126 0.159
Expression system: Escherichia coli BL21(DE3)

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