› 3t80

X-ray diffraction
2.5Å resolution

Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium bound to cytidine

Released:
DOI: 10.2210/pdb3t80/pdb
PDB entry 3t80 coloured by chain, front view.
PDB entry 3t80 coloured by chain, side view.
PDB entry 3t80 coloured by chain, top view.
Source organism: Salmonella enterica subsp. enterica serovar Typhimurium
Entry authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID), Staker BL, Edwards TE

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-187277 (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: 162 amino acids
Theoretical weight: 17.19 KDa
Source organism: Salmonella enterica subsp. enterica serovar Typhimurium
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8ZMF7 (Residues: 1-159; Coverage: 100%)
Gene names: STM2929, ispF
Sequence domains: YgbB family
Structure domains: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Ligands and Environments

5 bound ligands:
Ligand ZN 6 x ZN
Ligand MG 8 x MG
Ligand CTN 6 x CTN
Ligand POP 2 x POP
Ligand EDO 14 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: C2
Unit cell:
a: 200.013Å b: 147.657Å c: 56.919Å
α: 90° β: 106.38° γ: 90°
R-values:
R R work R free
0.212 0.211 0.245
Expression system: Escherichia coli BL21(DE3)

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