9I1G | pdb_00009i1g

Crystal structure of zebrafish S100I2 in Mg2+-bound form

PDB DOI: https://doi.org/10.2210/pdb9I1G/pdb

Classification: SIGNALING PROTEIN
Organism(s): Danio rerio
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-01-16 Released: 2025-12-03
Deposition Author(s): Demou, M., Yatime, L.
Funding Organization(s): H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.243 (Depositor), 0.247 (DCC)
R-Value Work:
0.224 (Depositor), 0.227 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Teleost-specific ictacalcins exhibit similar structural organization, cation-dependent activation and transcriptional regulation as human S100 proteins

Hernandez, L., Paris, T., Demou, M., Birck, C., Begon, C., Rodriguez-Vidal, J.F., Tyrkalska, S.D., Bureau, C., Gonzalez, C., Gracia, J., Lelievre, E., Mulero, V., Nguyen-Chi, M., Yatime, L.

(2025) FEBS J

DOI: https://doi.org/10.1111/febs.70354

Macromolecule Content

Total Structure Weight: 21.76 kDa
Atom Count: 1,493
Modeled Residue Count: 177
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein S100	A, B	99	Danio rerio	Mutation(s): 0 Gene Names: icn2, Icn2, zgc:171263
UniProt
Find proteins for A3FKT8 (Danio rerio) Explore A3FKT8 Go to UniProtKB: A3FKT8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3FKT8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.243 (Depositor), 0.247 (DCC)
R-Value Work: 0.224 (Depositor), 0.227 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.58	α = 90
b = 58.28	β = 91.59
c = 41.66	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
BALBES	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-03

Deposition Author(s):

Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	955576

Revision History (Full details and data files)

Version 1.0: 2025-12-03
Type: Initial release

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.