› 3f6m

X-ray diffraction
2.96Å resolution

Crystal Structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF from Yersinia pestis

Released:
DOI: 10.2210/pdb3f6m/pdb
PDB entry 3f6m coloured by chain, front view.
PDB entry 3f6m coloured by chain, side view.
PDB entry 3f6m coloured by chain, top view.
Source organism: Yersinia pestis CO92
Entry authors: Kim Y, Maltseva N, Stam J, Anderson WF, Joachimiak A, Center for Structural Genomics of Infectious Diseases (CSGID)

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-187190 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Chain: A
Molecule details ›
Chain: A
Length: 165 amino acids
Theoretical weight: 17.66 KDa
Source organism: Yersinia pestis CO92
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8ZBP7 (Residues: 1-162; Coverage: 100%)
Gene names: YPO3360, YP_0327, ispF, y0829
Sequence domains: YgbB family
Structure domains: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Ligands and Environments

No bound ligands
1 modified residue:
Ligand MSE 4 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: I213
Unit cell:
a: 146.64Å b: 146.64Å c: 146.64Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.194 0.203
Expression system: Escherichia coli

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