3DQO

Structure of the Yellow Fluorescent Protein Citrine Frozen at 1 Atmosphere Number 2: Structure 2 in a Series of 26 High Pressure Structures

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Alteration of citrine structure by hydrostatic pressure explains the accompanying spectral shift.

Barstow, B., Ando, N., Kim, C.U., Gruner, S.M.

(2008) Proc.Natl.Acad.Sci.Usa 105: 13362-13366

  • DOI: 10.1073/pnas.0802252105
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • A protein molecule is an intricate system whose function is highly sensitive to small external perturbations. However, no examples that correlate protein function with progressive subangstrom structural perturbations have thus far been presented. To ...

    A protein molecule is an intricate system whose function is highly sensitive to small external perturbations. However, no examples that correlate protein function with progressive subangstrom structural perturbations have thus far been presented. To elucidate this relationship, we have investigated a fluorescent protein, citrine, as a model system under high-pressure perturbation. The protein has been compressed to produce deformations of its chromophore by applying a high-pressure cryocooling technique. A closely spaced series of x-ray crystallographic structures reveals that the chromophore undergoes a progressive deformation of up to 0.8 A at an applied pressure of 500 MPa. It is experimentally demonstrated that the structural motion is directly correlated with the progressive fluorescence shift of citrine from yellow to green under these conditions. This protein is therefore highly sensitive to subangstrom deformations and its function must be understood at the subangstrom level. These results have significant implications for protein function prediction and biomolecule design and engineering, because they suggest methods to tune protein function by modification of the protein scaffold.

    Related Citations: 
    • High-pressure cooling of protein crystals without cryoprotectants.
      Kim, C.U.,Kapfer, R.,Gruner, S.M.
      (2005) Acta Crystallogr.,Sect.D 61: 881

    Organizational Affiliation: 

    School of Applied Physics, Department of Physics, and Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Green fluorescent protein
A
243Aequorea victoriaMutation(s): 5 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CR2
Query on CR2
A
L-PEPTIDE LINKINGC13 H13 N3 O4GLY, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.387α = 90.00
b = 62.379β = 90.00
c = 70.660γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
ADSCdata collection
MOSFLMdata reduction
REFMACrefinement
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2008-07-09 
  • Released Date: 2008-09-23 
  • Deposition Author(s): Barstow, B., Kim, C.U.

Revision History 

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance