1AQB

RETINOL-BINDING PROTEIN (RBP) FROM PIG PLASMA


Experimental Data Snapshot

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

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

    Department of Organic Chemistry, University of Padova and Biopolymer Research Center, CNR, 35131 Padova, Italy. [email protected]


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RETINOL-BINDING PROTEIN183Sus scrofa domesticusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P27485 (Sus scrofa)
Explore P27485 
Go to UniProtKB:  P27485
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27485
Sequence Annotations
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  • Reference Sequence
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 = 45.81α = 90
b = 53.137β = 90
c = 72.966γ = 90
Software Package:
Software NamePurpose
SAINTdata scaling
SAINTdata reduction
SHELXL-93model building
X-PLORmodel building
SHELXL-93refinement
X-PLORrefinement
SHELXL-93phasing
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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