3P28 | pdb_00003p28

Structure of a Circular Permutant of Green Fluorescent Protein

• PDB DOI: https://doi.org/10.2210/pdb3P28/pdb

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


• Deposited: 2010-10-01 Released: 2011-10-05 
• Deposition Author(s): Melief, E.H., Kim, H., Kim, T.S., Wachter, R.M., Tonge, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.237 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Construction and Characterization of a Stable Circular Permutant of Green Fluorescent Protein

Melief, E.H., Kim, H., Kim, T.S., Wachter, R.M., Tonge, P.J.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 27.24 kDa 
• Atom Count: 2,186 
• Modeled Residue Count: 235 
• Deposited Residue Count: 239 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A	239	Aequorea victoria	Mutation(s): 6  Gene Names: GFP
UniProt
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
GYS	A	L-PEPTIDE LINKING	C14 H15 N3 O5		SER, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.237 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.456	α = 90
b = 71.028	β = 90
c = 76.894	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASES	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-05 
Deposition Author(s): Melief, E.H., Kim, H., Kim, T.S., Wachter, R.M., Tonge, P.J.

Revision History  

• Version 1.0: 2011-10-05
  Type: Initial release
  
• Version 1.1: 2014-03-05
  Changes: Structure summary
• Version 1.2: 2017-06-21
  Changes: Database references, Source and taxonomy
• Version 2.0: 2023-11-15
  Changes: Advisory, Atomic model, Data collection, Database references
• Version 2.1: 2024-11-27
  Changes: Structure summary