9V56 | pdb_00009v56

Light driven bicarbonate reduction by fluorescent protein mRuby

PDB DOI: https://doi.org/10.2210/pdb9V56/pdb

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

Deposited: 2025-05-25 Released: 2026-05-27
Deposition Author(s): Dong, J.S.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.265 (Depositor), 0.283 (DCC)
R-Value Work:
0.214 (Depositor), 0.233 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Observation of light driven CO2 photoreduction by fluorescent protein mRuby

Dong, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 24.69 kDa
Atom Count: 1,766
Modeled Residue Count: 220
Deposited Residue Count: 220
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
fluorescent protein mRuby	A	220	Entacmaea quadricolor	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCT (Subject of Investigation/LOI) Query on BCT 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]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.265 (Depositor), 0.283 (DCC)
R-Value Work: 0.214 (Depositor), 0.233 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.37	α = 90
b = 66.74	β = 90
c = 94.78	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-27

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: 2026-05-27
Type: Initial release

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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.