3JUP

Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with (S)-5-bromo-2-(piperidin-3-ylamino)benzoic acid

• PDB DOI: https://doi.org/10.2210/pdb3JUP/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Burkholderia lata
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-15 Released: 2009-09-29 
• Deposition Author(s): Mentel, M., Jain, I.H., Breinbauer, R., Blankenfeldt, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.218 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

Literature

The Active Site of an Enzyme Can Host Both Enantiomers of a Racemic Ligand Simultaneously

Mentel, M., Blankenfeldt, W., Breinbauer, R.

(2009) Angew Chem Int Ed Engl 48: 9084-9087

• PubMed: 19876985 
• DOI: https://doi.org/10.1002/anie.200902997
• Primary Citation of Related Structures:  
  3JUM, 3JUN, 3JUO, 3JUP, 3JUQ

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Organizational Affiliation: 

Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 43.66 kDa 
• Atom Count: 2,890 
• Modelled Residue Count: 314 
• Deposited Residue Count: 370 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenazine biosynthesis protein A/B	A, B	185	Burkholderia lata	Mutation(s): 0  Gene Names: Bcep18194_B1568
UniProt
Find proteins for Q396C9 (Burkholderia lata (strain ATCC 17760 / DSM 23089 / LMG 22485 / NCIMB 9086 / R18194 / 383)) Explore Q396C9  Go to UniProtKB:  Q396C9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKD	C [auth A], D [auth B]	5-bromo-2-[(3S)-piperidin-3-ylamino]benzoate C12 H14 Br N2 O2 DFYNENBDVWMLFE-VIFPVBQESA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
AKD	PDBBind:  3JUP	Kd: 2630 (nM) from 1 assay(s)
	Binding MOAD:  3JUP	Kd: 2630 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.218 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.72	α = 90
b = 64.72	β = 90
c = 160.76	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-29 
Deposition Author(s): Mentel, M., Jain, I.H., Breinbauer, R., Blankenfeldt, W.

Revision History  

• Version 1.0: 2009-09-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations