3GHZ

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium

• PDB DOI: https://doi.org/10.2210/pdb3GHZ/pdb

• Classification: LYASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-04 Released: 2009-03-17 
• Deposition Author(s): Osipiuk, J., Gu, M., Peterson, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.205 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Starting Model: experimental

Literature

X-ray crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium.

Osipiuk, J., Gu, M., Peterson, S., Anderson, W.F., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.04 kDa 
• Atom Count: 3,823 
• Modelled Residue Count: 465 
• Deposited Residue Count: 486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	A, B, C	162	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: ispF, STM2929 EC: 4.6.1.12
UniProt
Find proteins for Q8ZMF7 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZMF7  Go to UniProtKB:  Q8ZMF7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POP	G [auth B]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
GOL	D [auth A], I [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	E [auth A], F [auth A], H [auth B], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.205 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: I 2 3
• Diffraction Data: https://doi.org/10.18430/m33ghz

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.974	α = 90
b = 143.974	β = 90
c = 143.974	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
MOLREP	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-17 
Deposition Author(s): Osipiuk, J., Gu, M., Peterson, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-03-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description