1J7X | pdb_00001j7x

CRYSTAL STRUCTURE OF A FUNCTIONAL UNIT OF INTERPHOTORECEPTOR RETINOID-BINDING PROTEIN (IRBP)

• PDB DOI: https://doi.org/10.2210/pdb1J7X/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Xenopus laevis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-05-19 Released: 2002-02-20 
• Deposition Author(s): Loew, A., Gonzalez-Fernandez, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.220 (Depositor) 
• R-Value Work: 
  0.205 (Depositor) 
• R-Value Observed: 
  0.207 (Depositor) 

Literature

Crystal structure of the functional unit of interphotoreceptor retinoid binding protein.

Loew, A., Gonzalez-Fernandez, F.

(2002) Structure 10: 43-49

• PubMed: 11796109 
• DOI: https://doi.org/10.1016/s0969-2126(01)00698-0
• Primary Citation Related Structures: 
  1J7X


• PubMed Abstract: 
  

  Interphotoreceptor retinoid binding protein (IRBP), the major soluble component of the interphotoreceptor matrix, is critical to the function, integrity, and development of the vertebrate retina. Although its role is poorly understood, IRBP has been thought to protect 11-cis retinal and all-trans retinol while facilitating their exchange between the photoreceptors and retinal-pigmented epithelium. We determined the X-ray structure of one of the functional units, or modules, of Xenopus laevis IRBP to 1.8 A resolution by multiwavelength anomalous dispersion. The monomeric protein consists of two domains separated by a hydrophobic ligand binding site. A structural homology to the recently solved photosystem II D1 C-terminal-processing protease and the enoyl-CoA isomerase/hydratase family suggests the utility of a common fold used in diverse settings, ranging from proteolysis to fatty acid isomerization to retinoid transport.

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Organizational Affiliation: 
• Department of Biochemistry, University of Texas, Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.51 kDa 
• Atom Count: 2,485 
• Modeled Residue Count: 302 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INTERPHOTORECEPTOR RETINOID-BINDING PROTEIN	A	302	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for Q7SZI7 (Xenopus laevis) Explore Q7SZI7  Go to UniProtKB:  Q7SZI7

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.220 (Depositor) 
• R-Value Work:  0.205 (Depositor) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.144	α = 90
b = 65.756	β = 90
c = 68.174	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-02-20 
Deposition Author(s): Loew, A., Gonzalez-Fernandez, F.

Revision History  

• Version 1.0: 2002-02-20
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary