3D96

Crystal Structure of the R132K:Y134F Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.71 Angstroms Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of site-directed mutants of cellular retinoic acid-binding protein II addresses the relationship between structural integrity and ligand binding.

Vaezeslami, S.Jia, X.Vasileiou, C.Borhan, B.Geiger, J.H.

(2008) Acta Crystallogr.,Sect.D 64: 1228-1239

  • DOI: 10.1107/S0907444908032216
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structural integrity of cellular retinoic acid-binding protein II (CRABPII) has been investigated using the crystal structures of CRABPII mutants. The overall fold was well maintained by these CRABPII mutants, each of which carried multiple diffe ...

    The structural integrity of cellular retinoic acid-binding protein II (CRABPII) has been investigated using the crystal structures of CRABPII mutants. The overall fold was well maintained by these CRABPII mutants, each of which carried multiple different mutations. A water-mediated network is found to be present across the large binding cavity, extending from Arg111 deep inside the cavity to the alpha2 helix at its entrance. This chain of interactions acts as a ;pillar' that maintains the integrity of the protein. The disruption of the water network upon loss of Arg111 leads to decreased structural integrity of the protein. A water-mediated network can be re-established by introducing the hydrophilic Glu121 inside the cavity, which results in a rigid protein with the alpha2 helix adopting an altered conformation compared with wild-type CRABPII.


    Related Citations: 
    • Determining Crystal Structures of Proteins and Protein Complexes by X-Ray Crystallography: X-Ray Crystallographic Studies of the Mutants of Cellular Retinoic Acid Binding Protein Type II Toward Designing a Mimic of Rhodopsin
      Vaezeslami, S.
      () Thesis --: --


    Organizational Affiliation

    Rigaku Americas Corporation, 9009 New Trails Drive, The Woodlands, TX 77381, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cellular retinoic acid-binding protein 2
A, B
137Homo sapiensMutation(s): 2 
Gene Names: CRABP2
Find proteins for P29373 (Homo sapiens)
Go to Gene View: CRABP2
Go to UniProtKB:  P29373
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.153 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 34.590α = 73.90
b = 37.230β = 74.82
c = 58.770γ = 87.90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
REFMACphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description