5NHN | pdb_00005nhn

Super-Folder Green Fluorescent Protein Artificiall dimer linked via 148 position

• PDB DOI: https://doi.org/10.2210/pdb5NHN/pdb

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


• Deposited: 2017-03-22 Released: 2018-09-26 
• Deposition Author(s): Worthy, H.L., Rizkallah, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.209 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Positive functional synergy of structurally integrated artificial protein dimers assembled by Click chemistry

Worthy, H.L., Auhim, H.S., Jamieson, W.D., Pope, J.R., Wall, A., Batchelor, R., Johnson, R.L., Watkins, D.W., Rizkallah, P.J., Castell, O.K., Jones, D.D.

(2019) Commun Chem 

• DOI: https://doi.org/10.1038/s42004-019-0185-5

Biological Assembly 1  

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

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

Biological Assembly Evidence: cross-linking, gel filtration

Macromolecule Content 

• Total Structure Weight: 52.03 kDa 
• Atom Count: 3,892 
• Modeled Residue Count: 454 
• Deposited Residue Count: 456 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A [auth B]	228	Aequorea victoria	Mutation(s): 6  Gene Names: gfp
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	B [auth A]	228	Aequorea victoria	Mutation(s): 6  Gene Names: gfp
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DB5	C [auth B]	[(4~{S})-4,5,6,7,8,9-hexahydro-1~{H}-cycloocta[d][1,2,3]triazol-4-yl] hydrogen carbonate C9 H13 N3 O3 ZBJGIWFCJONVKZ-ZETCQYMHSA-N
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	E [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRO	A [auth B]	L-PEPTIDE LINKING	C15 H17 N3 O5		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.209 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.8	α = 90
b = 99.8	β = 90
c = 108.92	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-26 
Deposition Author(s): Worthy, H.L., Rizkallah, P.J.

Revision History  

• Version 1.0: 2018-09-26
  Type: Initial release
  
• Version 1.1: 2019-07-31
  Changes: Data collection, Database references
• Version 1.2: 2019-10-16
  Changes: Data collection
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary