9FEL | pdb_00009fel

LSSmCherry1 - Directionality of Optical Properties of Fluorescent Proteins

• PDB DOI: https://doi.org/10.2210/pdb9FEL/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Discosoma sp.
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-21 Released: 2025-07-02 
• Deposition Author(s): Myskova, J., Brynda, J., Lazar, J.
• Funding Organization(s): Ministry of Education, Youth and Sports of the Czech Republic, Czech Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.213 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.189 (Depositor) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Directionality of Optical Properties of Fluorescent Proteins

Myskova, J., Brynda, J., Khoroshyy, P., Lazar, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 61.1 kDa 
• Atom Count: 3,916 
• Modeled Residue Count: 430 
• Deposited Residue Count: 532 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PAmCherry1 protein	A, B [auth L]	266	Discosoma sp.	Mutation(s): 0  Gene Names: PAmCherry, PAmCherry1
UniProt
Find proteins for D1MPT3 (Discosoma sp.) Explore D1MPT3  Go to UniProtKB:  D1MPT3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BME	C [auth A], G [auth L]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NRQ	A, B [auth L]	L-PEPTIDE LINKING	C16 H17 N3 O4 S		MET, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.213 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.189 (Depositor) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.54	α = 90
b = 107.98	β = 103.95
c = 58.73	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Myskova, J., Brynda, J., Lazar, J.

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Funding Organization	Location	Grant Number
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	CZ.02.1.01/0.0/0.0/16_019/0000729
Czech Science Foundation	Czech Republic	23-05983S

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release