9CJM | pdb_00009cjm

Red fluorescent protein mRuby3

PDB DOI: https://doi.org/10.2210/pdb9CJM/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Entacmaea quadricolor
Expression System: Escherichia phage EcSzw-2
Mutation(s): No

Deposited: 2024-07-07 Released: 2025-10-08
Deposition Author(s): Huang, M., Ng, H.L., Geisbrecht, B.V., Duan, H., Deng, M., Chu, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.306 (Depositor), 0.300 (DCC)
R-Value Work:
0.278 (Depositor), 0.271 (DCC)
R-Value Observed:
0.280 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9CJM

This is version 2.0 of the entry. See complete history.

Literature

Crystal model of the red fluorescent protein mRuby3

Huang, M., Deng, M., Zhang, S., Geisbrecht, B.V., Zou, Y., Duan, H., Lin, M., Ng, H.L., Chu, J.

To be published.

Macromolecule Content

Total Structure Weight: 106.35 kDa
Atom Count: 7,082
Modeled Residue Count: 876
Deposited Residue Count: 940
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Red fluorescent protein mRuby3	A, B, C, D	235	Entacmaea quadricolor	Mutation(s): 0
UniProt
Find proteins for Q8ISF8 (Entacmaea quadricolor) Explore Q8ISF8 Go to UniProtKB: Q8ISF8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ISF8
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 E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NRQ Query on NRQ	A, B, C, D	L-PEPTIDE LINKING	C₁₆ H₁₇ N₃ O₄ S		MET, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.306 (Depositor), 0.300 (DCC)
R-Value Work: 0.278 (Depositor), 0.271 (DCC)
R-Value Observed: 0.280 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.998	α = 90
b = 101.494	β = 90
c = 273.681	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

Geisbrecht, B.V.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-10-08
Type: Initial release
Version 2.0: 2026-03-18
Changes: Polymer sequence

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.