8J2K | pdb_00008j2k

Crystal structure of a bright green fluorescent protein (StayGold) with double mutation (N137A, Q140S) in jellyfish Cytaeis uchidae from Biortus

PDB DOI: https://doi.org/10.2210/pdb8J2K/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Cytaeis uchidae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-04-14 Released: 2023-12-13
Deposition Author(s): Wu, J., Wang, F., Gui, W., Cheng, W., Yang, Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.183 (Depositor), 0.190 (DCC)
R-Value Work:
0.153 (Depositor), 0.160 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a bright green fluorescent protein (StayGold) in jellyfish Cytaeis uchidae from Biortus

Wu, J., Wang, F., Gui, W., Cheng, W., Yang, Y.

To be published.

Macromolecule Content

Total Structure Weight: 55.54 kDa
Atom Count: 4,099
Modeled Residue Count: 429
Deposited Residue Count: 484
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
StayGold(N137A, Q140S)	A, B	242	Cytaeis uchidae	Mutation(s): 0
UniProt
Find proteins for A0A8S0GSD4 (Cytaeis uchidae) Explore A0A8S0GSD4 Go to UniProtKB: A0A8S0GSD4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8S0GSD4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CR2 Query on CR2	A, B	L-PEPTIDE LINKING	C₁₃ H₁₃ N₃ O₄		GLY, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.183 (Depositor), 0.190 (DCC)
R-Value Work: 0.153 (Depositor), 0.160 (DCC)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.789	α = 90
b = 134.789	β = 90
c = 59.18	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-12-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-12-13
Type: Initial release
Version 1.1: 2024-11-20
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.