1G7K

CRYSTAL STRUCTURE OF DSRED, A RED FLUORESCENT PROTEIN FROM DISCOSOMA SP. RED


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0-A resolution.

Yarbrough, D.Wachter, R.M.Kallio, K.Matz, M.V.Remington, S.J.

(2001) Proc.Natl.Acad.Sci.USA 98: 462-467

  • DOI: 10.1073/pnas.98.2.462

  • PubMed Abstract: 
  • The crystal structure of DsRed, a red fluorescent protein from a corallimorpharian, has been determined at 2.0-A resolution by multiple-wavelength anomalous dispersion and crystallographic refinement. Crystals of the selenomethionine-substituted prot ...

    The crystal structure of DsRed, a red fluorescent protein from a corallimorpharian, has been determined at 2.0-A resolution by multiple-wavelength anomalous dispersion and crystallographic refinement. Crystals of the selenomethionine-substituted protein have space group P2(1) and contain a tetramer with 222 noncrystallographic symmetry in the asymmetric unit. The refined model has satisfactory stereochemistry and a final crystallographic R factor of 0.162. The protein, which forms an obligatory tetramer in solution and in the crystal, is a squat rectangular prism comprising four protomers whose fold is extremely similar to that of the Aequorea victoria green fluorescent protein despite low ( approximately 23%) amino acid sequence homology. The monomer consists of an 11-stranded beta barrel with a coaxial helix. The chromophores, formed from the primary sequence -Gln-Tyr-Gly- (residues 66-68), are arranged in a approximately 27 x 34-A rectangular array in two approximately antiparallel pairs. The geometry at the alpha carbon of Gln-66 (refined without stereochemical restraints) is consistent with an sp(2) hybridized center, in accord with the proposal that red fluorescence is because of an additional oxidation step that forms an acylimine extension to the chromophore [Gross, L. A., Baird, G. S., Hoffman, R. C., Baldridge, K. K. & Tsien, R. Y. (2000) Proc. Natl. Acad. Sci. USA 87, 11990-11995]. The carbonyl oxygen of Phe-65 is almost 90 degrees out of the plane of the chromophore, consistent with theoretical calculations suggesting that this is the minimum energy conformation of this moiety despite the conjugation of this group with the rest of the chromophore.


    Related Citations: 
    • The Structure of the Chromophore within DsRed, a Red Fluorescent Protein from Coral
      Gross, L.A.,Baird, G.S.,Hoffman, R.C.,Baldridge, K.K.,Tsien, R.Y.
      (2000) Proc.Natl.Acad.Sci.USA 97: 11990
    • Fluorescent Proteins from Nonbioluminescent Anthozoa Species
      Matz, M.V.,Fradkov, A.F.,Labas, Y.A.,Savitsky, A.P.,Zaraisky, A.G.,Markelov, M.L.,Lukyanov, S.A.
      (1999) Nat.Biotechnol. 17: 969


    Organizational Affiliation

    Departments of Physics and Biology and the Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FLUORESCENT PROTEIN FP583
A, B, C, D
236Discosoma sp.N/A
Find proteins for Q9U6Y8 (Discosoma sp.)
Go to UniProtKB:  Q9U6Y8
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CRQ
Query on CRQ
A, B, C, D
L-PEPTIDE LINKINGC16 H16 N4 O5GLN, TYR, GLY
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.366α = 90.00
b = 112.270β = 93.81
c = 70.691γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
FHSCALEdata scaling
SHARPphasing
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-12-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance