3DQ5

Structure of the Yellow Fluorescent Protein Citrine Frozen at 1960 Atmospheres: Structure 19 in a Series of 26 High Pressure Structures


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

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 U S A 105: 13362-13366

  • DOI: 10.1073/pnas.0802252105
  • Primary Citation of Related Structures:  
    3DPW, 3DQ8, 3DPX, 3DQ9, 3DPZ, 3DQ1, 3DQ2, 3DQ3, 3DQ4, 3DQ5

  • 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 D Biol Crystallogr 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Green fluorescent proteinA241Aequorea victoriaMutation(s): 6 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CR2
Query on CR2
AL-PEPTIDE LINKINGC13 H13 N3 O4GLY, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.549α = 90
b = 63.127β = 90
c = 71.464γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report



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
    Changes: Version format compliance