6MWJ | pdb_00006mwj

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0863

• PDB DOI: https://doi.org/10.2210/pdb6MWJ/pdb

• Classification: LYASE
• Organism(s): Burkholderia pseudomallei 1710b
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-10-29 Released: 2019-11-06 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

Literature

Analysis of Burkholderia pseudomallei IspF in complex with sulfapyridine, sulfamonomethoxine, ethoxzolamide and acetazolamide

Grote, D., Stewart, C.G., Daraji, D.G., Enayati, P., Braverman, K.N., Romanaggi, C., Bolejack, M.J., Yano, J.K., Abendroth, J., Dranow, D.M., Pierce, P.G., Lorimer, D.D., Horanyi, P.S., Staker, B.L., Edwards, T.E., Myler, P.J., Horn, J.R., Hagen, T.J.

(2025) Acta Crystallogr F Struct Biol Commun 81: 138-145

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 53.14 kDa 
• Atom Count: 3,835 
• Modeled Residue Count: 475 
• Deposited Residue Count: 498 
• 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	166	Burkholderia pseudomallei 1710b	Mutation(s): 0  Gene Names: ispF, BURPS1710b_2511 EC: 4.6.1.12
UniProt
Find proteins for Q3JRA0 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JRA0  Go to UniProtKB:  Q3JRA0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AZM (Subject of Investigation/LOI)	E [auth A]	5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE C4 H6 N4 O3 S2 BZKPWHYZMXOIDC-UHFFFAOYSA-N
DMS	F [auth A], H [auth B], J [auth C]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	D [auth A], G [auth B], I [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36mwj

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.05	α = 90
b = 67.4	β = 96.4
c = 60.21	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-11-06 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2019-11-06
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2025-04-09
  Changes: Database references, Structure summary