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

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), 0.239 (DCC)
R-Value Observed:
0.243 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5MWC

This is version 1.2 of the entry. See complete history.

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.

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

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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	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth D] SDF format, chain D SDF format, chain E [auth A] MOL2 format, chain C [auth D] MOL2 format, chain D MOL2 format, chain E [auth A] mmCIF format, chain C [auth D] mmCIF format, chain D mmCIF format, chain E [auth A]	C [auth D], D, E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth D] Focus chain D Focus chain E [auth A] Interactions & Density Focus chain C [auth D] Focus chain D Focus chain E [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CR2 Query on 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), 0.239 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-02-14

Deposition Author(s):

Nikolaeva, A.Y.

Korzhenevskiy, D.A.

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 (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.