5VNX

Crystal structure of an 8-amino-7-oxononanoate synthase from Burkholderia multivorans with a potential glycine-PLP-Lys242 cyclized intermediate or byproduct

• PDB DOI: https://doi.org/10.2210/pdb5VNX/pdb

• Classification: TRANSFERASE
• Organism(s): Burkholderia multivorans ATCC 17616
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-01 Released: 2017-05-17 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.167 
• R-Value Work: 0.146 
• R-Value Observed: 0.146 

Literature

Crystal structure of a 8-amino-7-oxononanoate synthase from Burkholderia multivorans with a potential glycine-PLP-Lys242 cyclized intermediate or byproduct

Conrady, D.G., Abendroth, J., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 125.78 kDa 
• Atom Count: 10,651 
• Modelled Residue Count: 1,177 
• Deposited Residue Count: 1,179 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
8-amino-7-oxononanoate synthase	A, B, C	393	Burkholderia multivorans ATCC 17616	Mutation(s): 0  Gene Names: bioF, Bmul_0373, BMULJ_02881 EC: 2.3.1.47
UniProt
Find proteins for A9AE46 (Burkholderia multivorans (strain ATCC 17616 / 249)) Explore A9AE46  Go to UniProtKB:  A9AE46

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEN	D [auth A], E [auth A], J [auth B], K [auth B], N [auth C]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
SO4	H [auth A], O [auth C], P [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	F [auth A], G [auth A], I [auth A], L [auth B], M [auth B], Q [auth C], R [auth C], S [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.167 
• R-Value Work: 0.146 
• R-Value Observed: 0.146 
• Space Group: C 2 2 2
• Diffraction Data: https://doi.org/10.18430/M35VNX

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.53	α = 90
b = 262.09	β = 90
c = 65.34	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-17 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-05-17
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Other, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations