5L12

Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase from BURKHOLDERIA PSEUDOMALLEI double mutant

• PDB DOI: https://doi.org/10.2210/pdb5L12/pdb

• Classification: LYASE
• Organism(s): Burkholderia pseudomallei 1106a
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-07-28 Released: 2017-11-01 
• Deposition Author(s): Blain, J.M., Raneiri, G., Walter, R.L., Hagen, T.J., Horn, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.204 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

Literature

Enzyme Engineering for the Development of a High-Throughput Temperature Screen of Burkholderia pseudomallei IspF Inhibitors

Blain, J.M., Raneiri, G., Walter, R.L., Hagen, T.J., Horn, J.R.

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: 50.77 kDa 
• Atom Count: 3,682 
• Modelled Residue Count: 459 
• Deposited Residue Count: 474 
• 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	158	Burkholderia pseudomallei 1106a	Mutation(s): 2  Gene Names: ispF, BURPS1106A_2400 EC: 4.6.1.12
UniProt
Find proteins for A3NWD9 (Burkholderia pseudomallei (strain 1106a)) Explore A3NWD9  Go to UniProtKB:  A3NWD9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth B], F [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.204 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.859	α = 90
b = 68.14	β = 96.57
c = 60.408	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-01 
Deposition Author(s): Blain, J.M., Raneiri, G., Walter, R.L., Hagen, T.J., Horn, J.R.

Revision History  

• Version 1.0: 2017-11-01
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references, Derived calculations