1AQB

RETINOL-BINDING PROTEIN (RBP) FROM PIG PLASMA

• PDB DOI: https://doi.org/10.2210/pdb1AQB/pdb

• Classification: RETINOL TRANSPORT
• Organism(s): Sus scrofa domesticus
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 1997-07-28 Released: 1998-01-28 
• Deposition Author(s): Zanotti, G., Panzalorto, M., Marcato, A., Malpeli, G., Folli, C., Berni, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.237 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

Structure of pig plasma retinol-binding protein at 1.65 A resolution.

Zanotti, G., Panzalorto, M., Marcato, A., Malpeli, G., Folli, C., Berni, R.

(1998) Acta Crystallogr D Biol Crystallogr 54: 1049-1052

• PubMed: 9757135 
• DOI: https://doi.org/10.1107/s0907444998002303
• Primary Citation of Related Structures:  
  1AQB


• PubMed Abstract: 
  

  The crystal structure of pig plasma retinol-binding protein (RBP) has been determined at 1.65 A resolution. The space group is P212121, with a = 45.81 (4), b = 53.14 (5), c = 72.97 (8) A and one protein molecule in the asymmetric unit. The structure has been solved using the molecular replacement method and refined with restrained least squares to an R factor of 0.1844 and an Rfree of 0.237 for 18 874 and 1001 independent reflections, respectively. The relatively high resolution structure of pig holoRBP has revealed some new structural details. Moreover, it has provided a description of the binding site for Cd2+, a metal ion which is required for protein crystallization. The hepta-coordination of the RBP-bound cadmium ion involves different residues of two symmetry-related RBP molecules, consistent with the participation of the cation in intermolecular interactions that in turn promote protein crystallization.

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Organizational Affiliation: 

Department of Organic Chemistry, University of Padova and Biopolymer Research Center, CNR, 35131 Padova, Italy. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 21.58 kDa 
• Atom Count: 1,573 
• Modelled Residue Count: 175 
• Deposited Residue Count: 183 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RETINOL-BINDING PROTEIN	A	183	Sus scrofa domesticus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P27485 (Sus scrofa) Explore P27485  Go to UniProtKB:  P27485

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RTL	C [auth A]	RETINOL C20 H30 O FPIPGXGPPPQFEQ-OVSJKPMPSA-N
CD	B [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.237 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.81	α = 90
b = 53.137	β = 90
c = 72.966	γ = 90

Software Package:

Software Name	Purpose
SAINT	data scaling
SAINT	data reduction
SHELXL-93	model building
X-PLOR	model building
SHELXL-93	refinement
X-PLOR	refinement
SHELXL-93	phasing
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-01-28 
Deposition Author(s): Zanotti, G., Panzalorto, M., Marcato, A., Malpeli, G., Folli, C., Berni, R.

Revision History  

• Version 1.0: 1998-01-28
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2023-08-02
  Changes: Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary