9XIS | pdb_00009xis

Structural evidence of thioacetate reduction by fluorescent protein mRuby-( mRuby-thioacetate structure3 )

PDB DOI: https://doi.org/10.2210/pdb9XIS/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Entacmaea quadricolor
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-11-03 Released: 2026-11-11
Deposition Author(s): Dong, J.S.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.247 (Depositor), 0.247 (DCC)
R-Value Work:
0.212 (Depositor), 0.222 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural evidence of thioacetate reduction by fluorescent protein mRuby

Dong, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 24.8 kDa
Atom Count: 1,875
Modeled Residue Count: 217
Deposited Residue Count: 217
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mRuby	A	217	Entacmaea quadricolor	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HM7 (Subject of Investigation/LOI) Query on HM7 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	3-methylthioethane-pyrazinedione C₈ H₁₀ N₂ O₃ S₂ NCFKEOIXWQTKQL-YVMONPNESA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Non-standard Monomers 1 Unique
ID	Chains	Type	Formula	2D Diagram
CH6 Query on CH6	A	L-PEPTIDE LINKING	C₁₆ H₁₉ N₃ O₄ S

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.247 (Depositor), 0.247 (DCC)
R-Value Work: 0.212 (Depositor), 0.222 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.929	α = 90
b = 65.874	β = 90
c = 94.046	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
autoPX	data reduction
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-11

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31900913

Revision History (Full details and data files)

Version 1.0: 2026-11-11
Type: Initial release