2HPW | pdb_00002hpw

Green fluorescent protein from Clytia gregaria

• PDB DOI: https://doi.org/10.2210/pdb2HPW/pdb

• Classification: LUMINESCENT PROTEIN
• Organism(s): Clytia gregaria
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-07-17 Released: 2006-09-12 
• Deposition Author(s): Stepanyuk, G., Liu, Z.J., Vysotski, S.E., Lee, J., Rose, J.P., Wang, B.C., Southeast Collaboratory for Structural Genomics (SECSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.203 (Depositor) 
• R-Value Work: 
  0.182 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Green Fluorescent Protein from Clytia Gregaria at 1.55 A resolution

Liu, Z.J., Markova, S.V., Frank, L.A., Stepanyuk, G., Vysotski, E.S., Rose, J.P., Wang, B.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 26.38 kDa 
• Atom Count: 2,062 
• Modeled Residue Count: 229 
• Deposited Residue Count: 233 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A	233	Clytia gregaria	Mutation(s): 0  Gene Names: GFP
UniProt
Find proteins for D7PM05 (Clytia gregaria) Explore D7PM05  Go to UniProtKB:  D7PM05

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: 1.55 Å
• R-Value Free:  0.203 (Depositor) 
• R-Value Work:  0.182 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.091	α = 90
b = 91.446	β = 90
c = 110.612	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-12 
Deposition Author(s): Stepanyuk, G., Liu, Z.J., Vysotski, S.E., Lee, J., Rose, J.P., Wang, B.C., Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

• Version 1.0: 2006-09-12
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2015-01-21
  Changes: Structure summary
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Advisory, Atomic model, Data collection, Derived calculations
• Version 2.1: 2023-12-27
  Changes: Advisory, Derived calculations
• Version 2.2: 2024-10-30
  Changes: Structure summary
• Version 3.0: 2026-03-18
  Changes: Polymer sequence