5L03 | pdb_00005l03

Crystal structure of 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE Synthase from BURKHOLDERIA PSEUDOMALLEI bound to L-tryptophan hydroxamate

• PDB DOI: https://doi.org/10.2210/pdb5L03/pdb

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


• Deposited: 2016-07-26 Released: 2017-11-08 
• Deposition Author(s): Blain, J.M., Ghose, D., Gorman, J.L., Goshu, G.M., Ranieri, G., Zhao, L., Bode, B., Meganathan, R., Walter, R.L., Hagen, T.J., Horn, J.R.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.200 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.179 (Depositor) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Synthesis and Characterization of the Burkholderia pseudomallei IspF Inhibitor L-tryptophan hydroxamate

Blain, J.M., Ghose, D., Gorman, J.L., Goshu, G.M., Ranieri, G., Zhao, L., Bode, B., Meganathan, R., 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: 50.98 kDa 
• Atom Count: 3,740 
• Modeled Residue Count: 450 
• 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	Mutation(s): 0  Gene Names: ispF, DP46_3085, ERS012314_03919, SY87_14040 EC: 4.6.1.12
UniProt
Find proteins for A0A069B2G5 (Burkholderia pseudomallei) Explore A0A069B2G5  Go to UniProtKB:  A0A069B2G5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6ZB	E [auth A]	N-hydroxy-L-tryptophanamide C11 H13 N3 O2 LBMAEBPZXXNKMZ-VIFPVBQESA-N
ZN	D [auth A], F [auth B], G [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
6ZB	BindingDB:  5L03	Kd: min: 2.40e+4, max: 8.48e+5 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.200 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.179 (Depositor) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.515	α = 90
b = 68.126	β = 96.93
c = 60.659	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 

& Funding Information

Deposition Data

• Released Date: 2017-11-08 
Deposition Author(s): Blain, J.M., Ghose, D., Gorman, J.L., Goshu, G.M., Ranieri, G., Zhao, L., Bode, B., Meganathan, R., Walter, R.L., Hagen, T.J., Horn, J.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1R15AI113653-01
National Science Foundation (NSF, United States)	United States	MCB-0953323

Revision History  

• Version 1.0: 2017-11-08
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Derived calculations, Refinement description