2Q60

Crystal structure of the ligand binding domain of polyandrocarpa misakiensis rxr in tetramer in absence of ligand

• PDB DOI: https://doi.org/10.2210/pdb2Q60/pdb

• Classification: TRANSCRIPTION
• Organism(s): Polyandrocarpa misakiensis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-06-04 Released: 2008-05-27 
• Deposition Author(s): Borel, F., De Groot, A., Juillan-Binard, C., De Rosny, E., Laudet, V., Pebay-Peyroula, E., Fontecilla-Camps, J.-C., Ferrer, J.-L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.325 
• R-Value Work: 0.269 
• R-Value Observed: 0.272 

Starting Model: experimental

Literature

Crystal structure of the ligand-binding domain of the retinoid X receptor from the ascidian polyandrocarpa misakiensis.

Borel, F., de Groot, A., Juillan-Binard, C., de Rosny, E., Laudet, V., Pebay-Peyroula, E., Fontecilla-Camps, J.C., Ferrer, J.L.

(2008) Proteins 74: 538-542

• PubMed: 19004016 
• DOI: https://doi.org/10.1002/prot.22294
• Primary Citation of Related Structures:  
  2Q60

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Organizational Affiliation: 

Laboratoire de Cristallographie et Cristallogenèse des Protéines, Institut de Biologie Structurale Jean-Pierre Ebel, 41 rue Jules Horowitz, F-38027 Grenoble, France. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 116.27 kDa 
• Atom Count: 6,256 
• Modelled Residue Count: 796 
• Deposited Residue Count: 1,032 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoid X receptor	A, B, C, D	258	Polyandrocarpa misakiensis	Mutation(s): 2  Gene Names: PmRXR
UniProt
Find proteins for Q9UAF1 (Polyandrocarpa misakiensis) Explore Q9UAF1  Go to UniProtKB:  Q9UAF1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.325 
• R-Value Work: 0.269 
• R-Value Observed: 0.272 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.26	α = 90
b = 96.12	β = 90
c = 151.72	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Borel, F., De Groot, A., Juillan-Binard, C., De Rosny, E., Laudet, V., Pebay-Peyroula, E., Fontecilla-Camps, J.-C., Ferrer, J.-L.

Revision History  

• Version 1.0: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references
• Version 1.3: 2023-08-30
  Changes: Data collection, Refinement description