1OPB

THE CRYSTAL STRUCTURES OF HOLO-AND APO-CELLULAR RETINOL BINDING PROTEIN II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of holo and apo-cellular retinol-binding protein II.

Winter, N.S.Bratt, J.M.Banaszak, L.J.

(1993) J.Mol.Biol. 230: 1247-1259

  • DOI: 10.1006/jmbi.1993.1239
  • Primary Citation of Related Structures:  1OPA

  • PubMed Abstract: 
  • Apo and holo-cellular retinol-binding protein II have been crystallized, and their crystal structures have been determined to 2.1 A and 1.9 A respectively. The apo and holo-crystals have different but related triclinic space groups. The X-ray phases ...

    Apo and holo-cellular retinol-binding protein II have been crystallized, and their crystal structures have been determined to 2.1 A and 1.9 A respectively. The apo and holo-crystals have different but related triclinic space groups. The X-ray phases for both structures were determined using the molecular replacement method. The crystal co-ordinates were refined to an R-factor of 0.200 for apo, and 0.173 for holo-cellular retinol-binding protein II. The holo and apo-models have nearly the same tertiary structures. Cellular retinol-binding protein II consists of a ten-stranded anti-parallel beta-barrel with the ligand binding cavity within the barrel. Two alpha-helices cover the open end of the beta-barrel making it almost solvent inaccessible. A single portal large enough to admit a water molecule was observed opening into the binding cavity. Exogenously added retinol was found within the cavity of each holo-cellular retinol-binding protein II molecule. Each retinol was surrounded by both polar and non-polar residues. The hydroxyl group of the bound retinol hydrogen bonds to the amide group of glutamine 108. The overall conformation of the bound retinol was derived from the four different molecules of holo-cellular retinol-binding protein II present in the triclinic form. The four copies of bound retinol had essentially the same conformation as found in crystalline retinaldehyde.


    Organizational Affiliation

    Department of Biochemistry, Medical School, University of Minnesota, Minneapolis 55455.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CELLULAR RETINOL BINDING PROTEIN II
A, B, C, D
134Rattus norvegicusGene Names: Rbp2 (Crbpii)
Find proteins for P06768 (Rattus norvegicus)
Go to UniProtKB:  P06768
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

Download SDF File 
Download CCD File 
A, B, C, D
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RETKd: 50 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.173 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 37.000α = 92.60
b = 64.600β = 102.90
c = 56.000γ = 92.50
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other