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

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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

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: gel filtration

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

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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Samygina, V.R., Subach, O.M., Vlaskina, A.V., Nikolaeva, A.Y., Subach, F.V.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release