2JAD

Yellow fluorescent protein - glutaredoxin fusion protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of Glutaredoxin Grx1P C30S Mutant from Yeast.

Hakansson, K.O.Winther, J.R.

(2007) Acta Crystallogr.,Sect.D 63: 288

  • DOI: 10.1107/S0907444906051675
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glutathionylated glutaredoxin Grx1p C30S mutant from yeast has been crystallized in space group C222(1) and a fusion protein between redox-sensitive yellow fluorescent protein (rxYFP) and Grx1p C30S has been crystallized in space group P6(4). The str ...

    Glutathionylated glutaredoxin Grx1p C30S mutant from yeast has been crystallized in space group C222(1) and a fusion protein between redox-sensitive yellow fluorescent protein (rxYFP) and Grx1p C30S has been crystallized in space group P6(4). The structure of the latter was solved by molecular replacement using the known rxYFP structure as a search model. The structure of the Grx1p moiety was built and the structure was refined against 2.7 A synchrotron data to an R(free) of 25.7%. There are no specific contacts between the two domains, indicating that the observed enhanced exchange of reduction equivalents between them arises from diffusion or from an enhanced collision rate in solution. The Grx1p structure thus obtained was subsequently used to solve the structure of the orthorhombic crystal, which could be refined against 2.0 A data to an R(free) of 24.3%. The structure of the glutathione-bound protein and the glutaredoxin domain in the fusion protein are similar. The covalent disulfide bond between the glutathione and protein is broken upon exposure to synchrotron radiation. The structure and the glutathione-binding mode are described and compared with existing crystallographic and nuclear magnetic resonance (NMR) structures of related glutaredoxins. Conserved residues are clustered on one side of the active site.


    Related Citations: 
    • Crystallisation of Mutant Forms of Glutaredoxin Grx1P from Yeast
      Hakansson, K.O.,Winther, J.R.
      (2006) Acta Crystallogr.,Sect.F 62: 920


    Organizational Affiliation

    Department of Molecular Biology, August Krogh Building, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen Ø, Denmark. kohakansson@aki.ku.dk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YELLOW FLUORESCENT PROTEIN GLUTAREDOXIN FUSION PROTEIN
A
364Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Aequorea victoria
This entity is chimeric
Mutation(s): 1 
Gene Names: GRX1, GFP
Find proteins for P25373 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25373
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PIA
Query on PIA
A
L-PEPTIDE LINKINGC14 H15 N3 O4ALA,TYR,GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.214 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 132.111α = 90.00
b = 132.111β = 90.00
c = 58.722γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
CNSrefinement
MOSFLMdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-20
    Type: Initial release
  • Version 1.1: 2014-10-22
    Type: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
  • Version 1.2: 2017-03-15
    Type: Source and taxonomy
  • Version 1.3: 2018-01-17
    Type: Data collection