3GEX | pdb_00003gex

1.6 angstrom crystal structure of fluorescent protein Cypet

• PDB DOI: https://doi.org/10.2210/pdb3GEX/pdb

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


• Deposited: 2009-02-26 Released: 2010-03-09 
• Deposition Author(s): Hu, X., Liu, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

1.6 angstrom crystal structure of fluorescent protein Cypet

Liu, R., Ding, Y., Hu, X.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.5 kDa 
• Atom Count: 2,087 
• Modeled Residue Count: 234 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A	242	Aequorea victoria	Mutation(s): 8  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
CRF	A	L-PEPTIDE LINKING	C17 H18 N4 O4		THR, TRP, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.907	α = 90
b = 63.011	β = 90
c = 71.424	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Hu, X., Liu, R.

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-01
  Changes: Data collection, Refinement description
• Version 1.4: 2023-11-22
  Changes: Data collection
• Version 1.5: 2024-11-20
  Changes: Structure summary