8B2Y | pdb_00008b2y

Structure of the weakly red fluorescent protein csiFP4 from Clytia simplex

• PDB DOI: https://doi.org/10.2210/pdb8B2Y/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Clytia
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-15 Released: 2023-09-27 
• Deposition Author(s): Depernet, H., Engilberge, S., Lambert, G., Gotthard, G., Shaner, N., Royant, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 
  0.232 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.211 (Depositor) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Structure of the weakly red fluorescent protein csiFP4 from Clytia simplex

Depernet, H., Engilberge, S., Lambert, G., Gotthard, G., Shaner, N., Royant, A.

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 107.14 kDa 
• Atom Count: 7,818 
• Modeled Residue Count: 925 
• Deposited Residue Count: 932 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CsiFP4 chain A	A, B, C, D	233	Clytia	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AA [auth C], BA [auth C], E [auth A], EA [auth D], F [auth A], FA [auth D], G [auth A], GA [auth D], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], X [auth C], Y [auth C], Z [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	CA [auth C], DA [auth C], HA [auth D], IA [auth D], N [auth A], O [auth A], P [auth A], W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRQ	A, B, C, D	L-PEPTIDE LINKING	C16 H16 N4 O5		GLN, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free:  0.232 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.211 (Depositor) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.904	α = 90
b = 182.904	β = 90
c = 155.87	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-27 
Deposition Author(s): Depernet, H., Engilberge, S., Lambert, G., Gotthard, G., Shaner, N., Royant, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-09-27
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-11-13
  Changes: Structure summary
• Version 3.0: 2026-03-04
  Changes: Polymer sequence, Refinement description