9IRJ | pdb_00009irj

X-ray structure of PSmOrange3 (trigonal form)

PDB DOI: https://doi.org/10.2210/pdb9IRJ/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Discosoma sp.
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-07-16 Released: 2025-07-09
Deposition Author(s): Samygina, V.R., Subach, O.M., Vlaskina, A.V., Nikolaeva, A.Y., Subach, F.V.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.210 (Depositor), 0.186 (DCC)
R-Value Work:
0.178 (Depositor), 0.185 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9IRJ

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

Literature

Genetically Encoded Orange-to-Far-red Photoconvertible Fluorescent Protein PSmOrange3

Subach, O.M., Samygina, V.R., Vlaskina, A.V., Nikolaeva, A.Y., Subach, F.V.

To be published.

Macromolecule Content

Total Structure Weight: 26.56 kDa
Atom Count: 1,755
Modeled Residue Count: 216
Deposited Residue Count: 233
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mOrange	A	233	Discosoma sp.	Mutation(s): 1
UniProt
Find proteins for D0VWW2 (Discosoma sp.) Explore D0VWW2 Go to UniProtKB: D0VWW2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VWW2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRO Query on CRO	A	L-PEPTIDE LINKING	C₁₅ H₁₇ N₃ O₅		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.210 (Depositor), 0.186 (DCC)
R-Value Work: 0.178 (Depositor), 0.185 (DCC)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.165	α = 90
b = 137.165	β = 90
c = 55.223	γ = 120

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-09

Deposition Author(s):

Nikolaeva, A.Y.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-07-09
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.