1QVY

Crystal structure of RhoGDI K(199,200)R double mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The impact of Lys-->Arg surface mutations on the crystallization of the globular domain of RhoGDI.

Czepas, J.Devedjiev, Y.Krowarsch, D.Derewenda, U.Otlewski, J.Derewenda, Z.S.

(2004) Acta Crystallogr.,Sect.D 60: 275-280

  • DOI: 10.1107/S0907444903026271

  • PubMed Abstract: 
  • The potential of rational surface mutagenesis for enhanced protein crystallization is being probed in an ongoing effort. In previous work, it was hypothesized that residues with high conformational entropy such as Glu and Lys are suitable targets for ...

    The potential of rational surface mutagenesis for enhanced protein crystallization is being probed in an ongoing effort. In previous work, it was hypothesized that residues with high conformational entropy such as Glu and Lys are suitable targets for surface mutagenesis, as they are rarely incorporated in crystal contacts or protein-protein interfaces. Previous experiments using Lys-->Ala, Glu-->Ala and Glu-->Asp mutants confirmed that mutated proteins were more likely to crystallize. In the present paper, the usefulness of Lys-->Arg mutations is studied. Several mutations of the globular domain of human RhoGDI were generated, including the single mutants K105R, K113R, K127R, K138R and K141R, the double mutants K(98,99)R and K(199,200)R and the triple mutants K(98,99,105)R and K(135,138,141)R. It is shown that Lys-->Arg mutants are more likely to crystallize than the wild-type protein, although not as likely as Lys-->Ala mutants. Out of the nine mutants tested, five produced diffracting crystals, including the K(199,200)R double mutant, which crystallized in a new space group and exceeded by approximately 1.0 A the resolution of the diffraction of the wild-type crystal. Major crystal contacts in the new lattice were created by the mutated epitope.


    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rho GDP-dissociation inhibitor 1
A, B, C, D
139Homo sapiensMutation(s): 2 
Gene Names: ARHGDIA (GDIA1)
Find proteins for P52565 (Homo sapiens)
Go to Gene View: ARHGDIA
Go to UniProtKB:  P52565
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 148.660α = 90.00
b = 58.240β = 92.49
c = 75.050γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
REFMACrefinement
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-02-10
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance