4YR7

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


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Autoinducer 2-binding periplasmic protein LuxP
A, B
345Vibrio harveyiMutation(s): 0 
Gene Names: luxP
UniProt
Find proteins for P54300 (Vibrio harveyi)
Explore P54300 
Go to UniProtKB:  P54300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54300
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1B
Query on A1B

Download Ideal Coordinates CCD File 
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 = 74.45α = 90
b = 85.23β = 90
c = 133.6γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited KingdomEP/D023343/1, EP/D023327/1, EP/E000614/1
Royal SocietyUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 2.0: 2017-09-13
    Changes: Advisory, Atomic model, Author supporting evidence, Derived calculations
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description