Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26.95 kDa 
• Atom Count: 2051 
• Residue Count: 227 
• Unique protein chains: 1

1Q4C

S65T Q80R T203C Green Fluorescent Protein (GFP) pH 8.5

• DOI: 10.2210/pdb1Q4C/pdb

• Classification: LUMINESCENT PROTEIN
• Organism(s): Aequorea victoria
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2003-08-02 Released: 2004-02-03 
• Deposition Author(s): Jain, R.K., Ranganathan, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.214 
• R-Value Work: 0.194 
• R-Value Observed: 0.194 

Literature

Local complexity of amino acid interactions in a protein core.

Jain, R.K., Ranganathan, R.

(2004) Proc Natl Acad Sci U S A 101: 111-116

• PubMed: 14684834 
• DOI: 10.1073/pnas.2534352100
• Primary Citation of Related Structures:  
  1Q4E, 1Q4D, 1Q4C, 1Q4B, 1Q4A, 1Q73


• PubMed Abstract: 
  

Atomic resolution structures of proteins indicate that the core is typically well packed, suggesting a densely connected network of interactions between amino acid residues. The combinatorial complexity of energetic interactions in such a network could be enormous, a problem that limits our ability to relate structure and function. Here, we report a case study of the complexity of amino acid interactions in a localized region within the core of the GFP, a particularly stable and tightly packed molecule. Mutations at three sites within the chromophore-binding pocket display an overlapping pattern of conformational change and are thermodynamically coupled, seemingly consistent with the dense network model. However, crystallographic and energetic analyses of coupling between mutations paint a different picture; pairs of mutations couple through independent "hotspots" in the region of structural overlap. The data indicate that, even in highly stable proteins, the core contains sufficient plasticity in packing to uncouple high-order energetic interactions of residues, a property that is likely general in proteins.

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Organizational Affiliation: 

Howard Hughes Medical Institute and Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9050, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green Fluorescent Protein	A	236	Aequorea victoria	Mutation(s): 3  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
CRO	A	L-PEPTIDE LINKING	C15 H17 N3 O5		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.214 
• R-Value Work: 0.194 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.88	α = 90
b = 62.43	β = 90
c = 68.906	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-08-02 
• Released Date: 2004-02-03 
Deposition Author(s): Jain, R.K., Ranganathan, R.

Revision History 

• Version 1.0: 2004-02-03
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance