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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 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 ...

    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.


    Related Citations: 
    • Crystal Structure of Liganded and Unliganded Forms of Bovine Plasma Retinol-Binding Protein
      Zanotti, G., Berni, R., Monaco, H.L.
      (1993) J Biol Chem 268: 10728
    • Crystal Structure of the Trigonal Form of Human Plasma Retinol-Binding Protein at 2.5 A Resolution
      Zanotti, G., Ottonello, S., Berni, R., Monaco, H.L.
      (1993) J Mol Biol 230: 613

    Organizational Affiliation

    Department of Organic Chemistry, University of Padova and Biopolymer Research Center, CNR, 35131 Padova, Italy. zanotti@pdchor.chor.unipd.it



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RETINOL-BINDING PROTEINA183Sus scrofa domesticusMutation(s): 0 
Find proteins for P27485 (Sus scrofa)
Explore P27485 
Go to UniProtKB:  P27485
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RTL
Query on RTL

Download CCD File 
A
RETINOL
C20 H30 O
FPIPGXGPPPQFEQ-OVSJKPMPSA-N
 Ligand Interaction
CD
Query on CD

Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
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

View Full Validation Report



Entry History 

Deposition Data

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