2JAD

Yellow fluorescent protein - glutaredoxin fusion protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.214 
  • R-Value Observed: 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 D Biol Crystallogr 63: 288

  • DOI: 10.1107/S0907444906051675
  • Primary Citation of Related Structures:  
    2JAC, 2JAD

  • 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 structure of the latter was solved by molecular replacement using the known rxYFP structure as a search model ...

    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 Struct Biol Cryst Commun 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
YELLOW FLUORESCENT PROTEIN GLUTAREDOXIN FUSION PROTEINA362Aequorea victoriaSaccharomyces cerevisiae
This entity is chimeric
Mutation(s): 1 
Gene Names: GFP
EC: 1.11.1.9 (UniProt), 2.5.1.18 (UniProt)
UniProt
Find proteins for P25373 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25373 
Go to UniProtKB:  P25373
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP42212P25373
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth 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: 2.70 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.111α = 90
b = 132.111β = 90
c = 58.722γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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