Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 27.39 kDa 
• Atom Count: 2094 
• Residue Count: 231 
• Unique protein chains: 1

3DQO

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

• DOI: 10.2210/pdb3DQO/pdb

• Classification: LUMINESCENT PROTEIN
• Organism(s): Aequorea victoria
• Expression System: Escherichia coli
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.259 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

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

• PubMed: 18768811 
• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A	241	Aequorea victoria	Mutation(s): 6  Gene Names: GFP
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CR2	A	L-PEPTIDE LINKING	C13 H13 N3 O4		GLY, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.259 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.387	α = 90
b = 62.379	β = 90
c = 70.66	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction

Structure Validation

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