4YP9 | pdb_00004yp9

Crystal Structure of LuxP In Complex With a Formose Derived AI-2 Analogue

• PDB DOI: https://doi.org/10.2210/pdb4YP9/pdb

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


• Deposited: 2015-03-12 Released: 2016-03-23 
• Deposition Author(s): McDonough, M.A., Sattin, S., Gardner, P.M., Liu, C., 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: 2.70 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

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

Sattin, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 79.12 kDa 
• Atom Count: 5,637 
• Modeled Residue Count: 679 
• Deposited Residue Count: 690 
• Unique protein chains: 1

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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1B	E [auth A], G [auth B]	1-deoxy-alpha-L-xylulofuranose-1,2-borate C5 H10 B O6 GNABZUZRGYHKDZ-VPENINKCSA-N
CA	F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.732	α = 90
b = 104.732	β = 90
c = 69.532	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-03-23 
Deposition Author(s): McDonough, M.A., Sattin, S., Gardner, P.M., Liu, C., Davis, B.G.

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	EP/D023343/1
Engineering and Physical Sciences Research Council	United Kingdom	EP/D023327/1
Engineering and Physical Sciences Research Council	United Kingdom	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: Atomic model, Author supporting evidence, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description