5JAY | pdb_00005jay

Crystal Structure of an 8-amino-7-oxononanoate Synthase from Burkholderia xenovorans

• PDB DOI: https://doi.org/10.2210/pdb5JAY/pdb

• Classification: TRANSFERASE
• Organism(s): Paraburkholderia xenovorans LB400
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-04-12 Released: 2016-04-20 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of an 8-amino-7-oxononanoate Synthase from Burkholderia xenovorans

Dranow, D.M., Conrady, D.G., Lorimer, D., Edwards, T.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 84.84 kDa 
• Atom Count: 5,985 
• Modeled Residue Count: 749 
• Deposited Residue Count: 804 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
8-amino-7-oxononanoate synthase	A, B	402	Paraburkholderia xenovorans LB400	Mutation(s): 1  Gene Names: bioF, Bxeno_A0198, Bxe_A4264 EC: 2.3.1.47
UniProt
Find proteins for Q146K3 (Paraburkholderia xenovorans (strain LB400)) Explore Q146K3  Go to UniProtKB:  Q146K3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35JAY

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.87	α = 90
b = 63.2	β = 90
c = 65.19	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-20 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-04-20
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description