9VSJ | pdb_00009vsj

Crystal structure of the genetically-encoded green calcium sensor icBTnC2 in its calcium bound-state

• PDB DOI: https://doi.org/10.2210/pdb9VSJ/pdb

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


• Deposited: 2025-07-08 Released: 2025-09-17 
• Deposition Author(s): Boyko, K.M., Nikolaeva, A.Y., Dorovatovskii, P.V., Vlaskina, A.V., Agapova, Y.K., Petrenko, D.E., Subach, O.M., Chelykhova, S.A., Popov, V.O., Subach, F.V.
• Funding Organization(s): Ministry of Science and Higher Education of the Russian Federation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.220 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the genetically-encoded green calcium sensor icBTnC2 in its calcium bound-state

Boyko, K.M., Nikolaeva, A.Y., Dorovatovskii, P.V., Vlaskina, A.V., Agapova, Y.K., Petrenko, D.E., Subach, O.M., Chelykhova, S.A., Popov, V.O., 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 PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.32 kDa 
• Atom Count: 2,671 
• Modeled Residue Count: 299 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
icBTnC2 - the genetically-encoded green calcium sensor based on the fluorescent protein mBaoJin and calcium binding domain of C-terminal minimal domain of troponin C from Calypte Anna	A	307	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CR2	A	L-PEPTIDE LINKING	C13 H13 N3 O4		GLY, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.220 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.697	α = 90
b = 128.697	β = 90
c = 52.737	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
gemmi	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-17 
Deposition Author(s): Boyko, K.M., Nikolaeva, A.Y., Dorovatovskii, P.V., Vlaskina, A.V., Agapova, Y.K., Petrenko, D.E., Subach, O.M., Chelykhova, S.A., Popov, V.O., Subach, F.V.

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Funding Organization	Location	Grant Number
Ministry of Science and Higher Education of the Russian Federation	Russian Federation	--

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release
  
• Version 2.0: 2026-03-18
  Changes: Polymer sequence