9F03 | pdb_00009f03

mRhubarb720-WT

PDB DOI: https://doi.org/10.2210/pdb9F03/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Rhodopseudomonas palustris
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-04-15 Released: 2025-10-29
Deposition Author(s): Aksakal, O., Rizkallah, P.J., Warren, A., Lipka-Lloyd, M., Jones, D.D.
Funding Organization(s): Engineering and Physical Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.309 (Depositor), 0.298 (DCC)
R-Value Work:
0.225 (Depositor), 0.230 (DCC)
R-Value Observed:
0.230 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Monomeric rhubarb fluorescent protein

Aksakal, O., Rizkallah, P.J., Jones, D.D.

To be published.

Macromolecule Content

Total Structure Weight: 33.88 kDa
Atom Count: 2,382
Modeled Residue Count: 304
Deposited Residue Count: 304
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mRhubarb720 fluorescent protein	A	304	Rhodopseudomonas palustris	Mutation(s): 7 Gene Names: iRFP
UniProt
Find proteins for G1FNL7 (Rhodopseudomonas palustris) Explore G1FNL7 Go to UniProtKB: G1FNL7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1FNL7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LBV (Subject of Investigation/LOI) Query on LBV 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-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid C₃₃ H₃₇ N₄ O₆ DKMLMZVDTGOEGU-ISEYCTJISA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.309 (Depositor), 0.298 (DCC)
R-Value Work: 0.225 (Depositor), 0.230 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.845	α = 90
b = 58.845	β = 90
c = 185.883	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-29

Deposition Author(s):

Rizkallah, P.J.

Lipka-Lloyd, M.

Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2025-10-29
Type: Initial release
Version 1.1: 2025-11-19
Changes: Data collection

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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.