6NMO

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

• PDB DOI: https://doi.org/10.2210/pdb6NMO/pdb

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


• Deposited: 2019-01-11 Released: 2020-01-15 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.159 
• R-Value Work: 0.126 
• R-Value Observed: 0.127 

Starting Model: experimental

Literature

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

Abendroth, J., Dranow, D.M., Pierce, P.G., Rouffet, M., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 52.84 kDa 
• Atom Count: 4,205 
• Modelled Residue Count: 478 
• Deposited Residue Count: 489 
• 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	163	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QMS	M [auth C]	N-(QUINOLIN-8-YL)METHANESULFONAMIDE C10 H10 N2 O2 S XYEPUTZVZYUENX-UHFFFAOYSA-N
MLI	F [auth A], G [auth B], K [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
DMS	E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	D [auth A], H [auth B], L [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	I [auth B], J [auth B], N [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.159 
• R-Value Work: 0.126 
• R-Value Observed: 0.127 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/m36nmo

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.08	α = 90
b = 67.6	β = 96.48
c = 60.81	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-15 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2020-01-15
  Type: Initial release
  
• Version 1.1: 2020-01-22
  Changes: Database references, Structure summary
• Version 1.2: 2020-03-11
  Changes: Data collection, Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description