6KL1 | pdb_00006kl1

Crystal structure of the S65T/F99S/M153T/V163A variant of non-deuterated GFP at pD 8.5

• PDB DOI: https://doi.org/10.2210/pdb6KL1/pdb

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


• Deposited: 2019-07-28 Released: 2019-12-11 
• Deposition Author(s): Tai, Y., Takaba, K., Hanazono, Y., Dao, H.A., Miki, K., Takeda, K.
• Funding Organization(s): Japan Society for the Promotion of Science, Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.85 Å
• R-Value Free: 
  0.118 (Depositor), 0.118 (DCC) 
• R-Value Work: 
  0.103 (Depositor), 0.103 (DCC) 
• R-Value Observed: 
  0.104 (Depositor) 

Starting Model: experimental

Literature

X-ray crystallographic studies on the hydrogen isotope effects of green fluorescent protein at sub-angstrom resolutions

Tai, Y., Takaba, K., Hanazono, Y., Dao, H.A., Miki, K., Takeda, K.

(2019) Acta Crystallogr D Biol Crystallogr 75: 1096-1106

• DOI: https://doi.org/10.1107/S2059798319014608

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 25.92 kDa 
• Atom Count: 3,176 
• Modeled Residue Count: 228 
• Deposited Residue Count: 229 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A	229	Aequorea victoria	Mutation(s): 4  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
CRO	A	L-PEPTIDE LINKING	C15 H17 N3 O5		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.85 Å
• R-Value Free:  0.118 (Depositor), 0.118 (DCC) 
• R-Value Work:  0.103 (Depositor), 0.103 (DCC) 
• R-Value Observed: 0.104 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.915	α = 90
b = 62.107	β = 90
c = 68.865	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SHELXL	refinement
DENZO	data reduction
MOLREP	phasing
PDB_EXTRACT	data extraction
SCALEPACK	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-12-11 
Deposition Author(s): Tai, Y., Takaba, K., Hanazono, Y., Dao, H.A., Miki, K., Takeda, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	17H03643
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	Photon and Quantum Basic Research Coordinated Development Program

Revision History  

• Version 1.0: 2019-12-11
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references
• Version 2.1: 2023-11-22
  Changes: Refinement description
• Version 2.2: 2024-11-06
  Changes: Structure summary
• Version 3.0: 2026-03-18
  Changes: Polymer sequence