Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 34614.80 
• Atom Count: 2017 
• Residue Count: 303 
• Unique protein chains: 1

4XGY

GFP based antibody (fluorobody)

• DOI: 10.2210/pdb4XGY/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Aequorea victoria
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 10 


• Deposited: 2015-01-03 Released: 2015-07-01 
• Deposition Author(s): Shi, N., Chen, Y.G., Wang, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.494 Å
• R-Value Free: 0.167 
• R-Value Work: 0.145 

Literature

The structure of a GFP-based antibody (fluorobody) to TLH, a toxin from Vibrio parahaemolyticus.

Chen, Y., Huang, X., Wang, R., Wang, S., Shi, N.

(2015) Acta Crystallogr.,Sect.F 71: 913-918

• PubMed: 26144238 
• DOI: 10.1107/S2053230X15008845


• PubMed Abstract: 
  

A fluorobody is a manmade hybrid molecule that is composed of green fluorescent protein (GFP) and a fragment of antibody, which combines the affinity and specificity of an antibody with the visibility of a GFP. It is able to provide a real-time indication of binding while avoiding the use of tags and secondary binding reagents. Here, the expression, purification and crystal structure of a recombinant fluorobody for TLH (thermolabile haemolysin), a toxin from the lethal food-borne disease bacterium Vibrio parahaemolyticus, are presented. This is the first structure of a fluorobody to be reported. Crystals belonging to space group P4(3)2(1)2, with unit-cell parameters a = b = 63.35, c = 125.90 Å, were obtained by vapour diffusion in hanging drops and the structure was refined to an Rfree of 16.7% at 1.5 Å resolution. The structure shows a CDR loop of the antibody on the GFP scaffold.

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Organizational Affiliation: 

State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yangqiao Road West, Fuzhou 350002, People's Republic of China.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Green fluorescent protein, mAb LCDR3, Green fluorescent protein	A	305	Aequorea victoria	Mutation(s): 10  Gene Names: gfp
Find proteins for A0A059PIQ0 (Aequorea victoria) Go to UniProtKB:  A0A059PIQ0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PE5	A	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL, POLYETHYLENE GLYCOL PEG400 C18 H38 O9 CUDPPTPIUWYGFI-UHFFFAOYSA-N

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: 1.494 Å
• R-Value Free: 0.167 
• R-Value Work: 0.145 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 63.350	α = 90.00
b = 63.350	β = 90.00
c = 125.900	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
iMOSFLM	data reduction
iMOSFLM	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-01-03 
• Released Date: 2015-07-01 
• Deposition Author(s): Shi, N., Chen, Y.G., Wang, S.H.

Revision History 

• Version 1.0: 2015-07-01
  Type: Initial release
• Version 1.1: 2015-07-22
  Type: Database references