7CZ0 | pdb_00007cz0

Crystal structure of a thermostable green fluorescent protein (TGP) with a synthetic nanobody (Sb92)

• PDB DOI: https://doi.org/10.2210/pdb7CZ0/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Galaxea fascicularis, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-09-06 Released: 2021-09-08 
• Deposition Author(s): Cai, H., Yao, H., Li, T., Hutter, C., Tang, Y., Li, Y., Seeger, M., Li, D.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 
  0.241 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

An improved fluorescent protein tag and its nanobodies for membrane protein expression, stability assay, and purification

Cai, H., Yao, H., Li, T., Hutter, C., Tang, Y., Li, Y., Seeger, M., Li, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 171.45 kDa 
• Atom Count: 10,620 
• Modeled Residue Count: 1,324 
• Deposited Residue Count: 1,504 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermostable green fluorescent protein (TGP)	A, B, C, D	232	Galaxea fascicularis	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthetic nanobody (Sybody) 92 recognizing the thermostable green fluorescent protein (TGP)	E, F, G, H	144	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAD	L [auth A]	CACODYLIC ACID C2 H7 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-N
CAC	U [auth D]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
GOL	I [auth A], J [auth A], K [auth A], M [auth A], N [auth B], O [auth B], Q [auth B], R [auth B], S [auth B], T [auth C], V [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	P [auth B], W [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRQ	A, B, C, D	L-PEPTIDE LINKING	C16 H16 N4 O5		GLN, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free:  0.241 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.245	α = 90
b = 130.154	β = 90
c = 171.453	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-09-08 
Deposition Author(s): Cai, H., Yao, H., Li, T., Hutter, C., Tang, Y., Li, Y., Seeger, M., Li, D.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	31870726

Revision History  

• Version 1.0: 2021-09-08
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2023-11-29
  Changes: Refinement description
• Version 2.2: 2024-10-16
  Changes: Structure summary
• Version 3.0: 2026-03-18
  Changes: Polymer sequence