Structure of the Yellow Fluorescent Protein Citrine Frozen at 1250 Atmospheres Number 3: Structure 13 in a Series of 26 High Pressure Structures

Experimental Data Snapshot

  • Resolution: 1.49 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1073/pnas.0802252105
  • Primary Citation of Related Structures:  
    3DPW, 3DPX, 3DPZ, 3DQ1, 3DQ2, 3DQ3, 3DQ4, 3DQ5, 3DQ6, 3DQ7, 3DQ8, 3DQ9, 3DQA, 3DQC, 3DQD, 3DQE, 3DQF, 3DQH, 3DQI, 3DQJ, 3DQK, 3DQL, 3DQM, 3DQN, 3DQO, 3DQU

  • 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 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Green fluorescent protein241Aequorea victoriaMutation(s): 6 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42212
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on CR2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.49 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.44α = 90
b = 63.356β = 90
c = 71.575γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
DPSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection