4LUR | pdb_00004lur

Crystal Structure of Zebrafish Interphotoreceptor Retinoid-Binding Protein (IRBP) Module 1

• PDB DOI: https://doi.org/10.2210/pdb4LUR/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Danio rerio
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-07-25 Released: 2014-12-10 
• Deposition Author(s): Ghosh, D., Gonzalez-Fernandez, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.268 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Structure of Zebrafish IRBP Reveals Its Fatty Acid Binding Sites and Retention of Protease Fold

Ghosh, D., Haswell, K.M., Sprada, M., Gonzalez-Fernandez, F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.7 kDa 
• Atom Count: 2,556 
• Modeled Residue Count: 309 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interphotoreceptor Retinoid-Binding Protein(IRBP)	A	309	Danio rerio	Mutation(s): 0
UniProt
Find proteins for F1Q9N9 (Danio rerio) Explore F1Q9N9  Go to UniProtKB:  F1Q9N9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLA	F [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
EPE	B [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 1.90 Å
• R-Value Free:  0.268 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.295	α = 90
b = 97.771	β = 90
c = 41.214	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
CCP4	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-10 
Deposition Author(s): Ghosh, D., Gonzalez-Fernandez, F.

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Advisory, Refinement description
• Version 1.2: 2023-09-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-10-30
  Changes: Structure summary