7CZ0

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free: 0.241
R-Value Work: 0.202
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAD Query on CAD Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A]	L [auth A]	CACODYLIC ACID C₂ H₇ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain U [auth D] MOL2 format, chain U [auth D]	U [auth D]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain U [auth D] Interactions & Density Focus chain U [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth C] SDF format, chain V [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth C] MOL2 format, chain V [auth D]	I [auth A] J [auth A] K [auth A] M [auth A] N [auth B] 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		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain V [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain V [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain W [auth D] MOL2 format, chain P [auth B] MOL2 format, chain W [auth D]	P [auth B], W [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain P [auth B] Focus chain W [auth D] Interactions & Density Focus chain P [auth B] Focus chain W [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRQ Query on 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
R-Value Work: 0.202
R-Value Observed: 0.204
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

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Entry History & Funding Information

Deposition Data

Released Date: 2021-09-08

Deposition Author(s):

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

Revision History (Full details and data files)

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

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Help and Resources

7CZ0

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

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

Entity ID: 1

Entity Groups

Sequence Annotations

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Entity ID: 2