9G7Q | pdb_00009g7q

Structure of the StayRose dimer

PDB DOI: https://doi.org/10.2210/pdb9G7Q/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Cytaeis uchidae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-07-22 Released: 2025-05-21
Deposition Author(s): Crow, A.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Wellcome Trust, Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 ?
R-Value Free:
0.178 (Depositor), 0.189 (DCC)
R-Value Work:
0.154 (Depositor), 0.167 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

StayRose: a photostable StayGold derivative red-shifted by genetic code expansion

Scott, W., Ivorra-Molla, E., Akhuli, D., Massam-Wu, T., Cook, J., Song, L., Mishima, M., Crow, A., Balasubramanian, M.K.

(2024) bioRxiv

DOI: https://doi.org/10.1101/2024.12.13.628370

Macromolecule Content

Total Structure Weight: 53.15 kDa
Atom Count: 4,155
Modeled Residue Count: 429
Deposited Residue Count: 454
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
StayRose	A, B	227	Cytaeis uchidae	Mutation(s): 2 Gene Names: CU17S
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], O [auth B], P [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain N [auth B]	C [auth A], N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain N [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1IJF Query on A1IJF	A, B	L-PEPTIDE LINKING	C₁₃ H₁₄ N₄ O₄		GLY, TY2, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 ?
R-Value Free: 0.178 (Depositor), 0.189 (DCC)
R-Value Work: 0.154 (Depositor), 0.167 (DCC)

Space Group: P 6₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 133.306	α = 90
b = 133.306	β = 90
c = 58.35	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-21

Deposition Author(s):

Crow, A.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/V017101/1
Wellcome Trust	United Kingdom	MA101885
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N014294/1