5MWC | pdb_00005mwc

Crystal structure of the genetically-encoded green calcium indicator NTnC in its calcium bound state

• PDB DOI: https://doi.org/10.2210/pdb5MWC/pdb

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


• Deposited: 2017-01-18 Released: 2018-02-14 
• Deposition Author(s): Boyko, K.M., Nikolaeva, A.Y., Korzhenevskiy, D.A., Rakitina, T.V., Popov, V.O., Subach, O.M., Barykina, N.V., Subach, F.V.
• Funding Organization(s): Russian Science Foundation, Russian Foundation for Basic Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.310 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: experimental

Literature

Enchanced variant of genetically-encoded green calcium indicator NTnC

Subach, O.M., Barykina, N.V., Piatkevich, K.D., Sotskov, V.P., Roshchina, M.A., Kunitsyna, T.A., Malyshev, A.Y., Varizhuk, A.M., Pozmogova, G.E., Anokhin, K.V., Enikolopov, G.N., Boyko, K.M., Nikolaeva, A.Y., Korzhenevskiy, D.A., Rakitina, T.V., 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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 70.22 kDa 
• Atom Count: 4,161 
• Modeled Residue Count: 530 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
genetically-encoded green calcium indicator NTnC	A [auth D], B [auth A]	309	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth D], D, E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.310 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.1	α = 90
b = 82.1	β = 90
c = 157.47	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MoRDa	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-02-14 
Deposition Author(s): Boyko, K.M., Nikolaeva, A.Y., Korzhenevskiy, D.A., Rakitina, T.V., Popov, V.O., Subach, O.M., Barykina, N.V., Subach, F.V.

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Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	14-24-00172
Russian Science Foundation	Russian Federation	16-15-10323
Russian Foundation for Basic Research	Russian Federation	15-04-03383

Revision History  

• Version 1.0: 2018-02-14
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary