Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 79.04 kDa 
• Atom Count: 5656 
• Modelled Residue Count: 679 
• Deposited Residue Count: 690 
• Unique protein chains: 1

4YR7

Structure of LuxP In Complex With 1-deoxy-alpha-L-xylulofuranose-1,2-borate

• DOI: 10.2210/pdb4YR7/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Vibrio harveyi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-03-14 Released: 2016-03-23 
• Deposition Author(s): McDonough, M.A., Sattin, S., Davis, B.G.
• Funding Organization(s): Engineering and Physical Sciences Research Council, Royal Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 0.203 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 

Literature

Discovery of Glycomimetic Agonists from a Protocell Metabolism, Proto-natural Product Libraries

Sattin, S., McDonough, M.A., Davis, B.G.

To be published.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Autoinducer 2-binding periplasmic protein LuxP	A, B	345	Vibrio harveyi	Mutation(s): 0  Gene Names: luxP
UniProt
Find proteins for P54300 (Vibrio harveyi) Explore P54300  Go to UniProtKB:  P54300

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1B	C [auth A], D [auth B]	1-deoxy-alpha-L-xylulofuranose-1,2-borate C5 H10 B O6 GNABZUZRGYHKDZ-VPENINKCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 0.203 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.45	α = 90
b = 85.23	β = 90
c = 133.6	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-03-14 
• Released Date: 2016-03-23 
Deposition Author(s): McDonough, M.A., Sattin, S., Davis, B.G.

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	EP/D023343/1, EP/D023327/1, EP/E000614/1
Royal Society	United Kingdom	--

Revision History  

• Version 1.0: 2016-03-23
  Type: Initial release
  
• Version 2.0: 2017-09-13
  Changes: Advisory, Atomic model, Author supporting evidence, Derived calculations