PDB-9i2n: Crystal structure of zebrafish S100I1 protein in apo form

ID or keywords:

Entry

Database: PDB / ID: 9i2n

Title

Crystal structure of zebrafish S100I1 protein in apo form

Components

Protein S100

Keywords

SIGNALING PROTEIN / S100 protein / alarmin / EF-hand motif / calcium-binding protein

Function / homology

Function and homology information

transition metal ion binding / calcium-dependent protein binding / calcium ion binding / cytoplasm
Similarity search - Function

Biological species

Danio rerio (zebrafish)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Paris, T. / Yatime, L.

Funding support

European Union, 1items

Citation

Journal: Febs J. / Year: 2025
Title: Teleost-specific ictacalcins exhibit similar structural organization, cation-dependent activation and transcriptional regulation as human S100 proteins
Authors: 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.

History

Deposition	Jan 21, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 3, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9i2n.cif.gz	167.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9i2n.ent.gz	135 KB	Display	PDB format
PDBx/mmJSON format	9i2n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9i2n_validation.pdf.gz	444.2 KB	Display	wwPDB validaton report
Full document	9i2n_full_validation.pdf.gz	447.3 KB	Display
Data in XML	9i2n_validation.xml.gz	24.3 KB	Display
Data in CIF	9i2n_validation.cif.gz	34.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i2/9i2n ftp://data.pdbj.org/pub/pdb/validation_reports/i2/9i2n	HTTPS FTP

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Related structure data

Related structure data	9hygC 9i1gC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Protein S100

B: Protein S100

C: Protein S100

D: Protein S100

42.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein S100

B: Protein S100

defined by author&software
Evidence: gel filtration
21.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Protein S100

D: Protein S100

defined by author&software
21.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	34.380, 131.010, 45.820
Angle α, β, γ (deg.)	90.00, 90.09, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Protein S100 / S100 calcium-binding protein Mass: 10548.120 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: icn, fa91d07, mg:cb02f02, s100a4a, wu:fa91d07 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XG62
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 491 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.71 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M Li sulfate, 0.1 M Tris-HCl pH 8.5, 25% PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 7, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.5→50 Å / Num. obs: 61980 / % possible obs: 96 % / Redundancy: 6.8 % / CC_1/2: 1 / R_rim(I) all: 0.054 / Net I/σ(I): 22.85
Reflection shell	Resolution: 1.5→1.57 Å / Redundancy: 6.09 % / Num. unique obs: 7421 / CC_1/2: 0.83 / R_rim(I) all: 0.75 / % possible all: 90.3

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→45.82 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.46 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2003	3120	5.06 %
R_work	0.1681	-	-
obs	0.1697	61633	95.46 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.5→45.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2834	0	0	492	3326

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2965
X-RAY DIFFRACTION	f_angle_d	1.039	3996
X-RAY DIFFRACTION	f_dihedral_angle_d	15.07	1114
X-RAY DIFFRACTION	f_chiral_restr	0.078	475
X-RAY DIFFRACTION	f_plane_restr	0.005	500

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.5-1.5235	0.3459	143	0.3662	2327	X-RAY DIFFRACTION	85
1.5235-1.5484	0.323	147	0.306	2416	X-RAY DIFFRACTION	88
1.5484-1.5751	0.2496	152	0.2175	2618	X-RAY DIFFRACTION	93
1.5751-1.6038	0.2611	120	0.2048	2588	X-RAY DIFFRACTION	94
1.6038-1.6346	0.2491	149	0.1999	2700	X-RAY DIFFRACTION	94
1.6346-1.668	0.2359	139	0.1927	2581	X-RAY DIFFRACTION	96
1.668-1.7043	0.2054	138	0.1787	2684	X-RAY DIFFRACTION	95
1.7043-1.7439	0.2022	127	0.1842	2657	X-RAY DIFFRACTION	95
1.7439-1.7875	0.2288	149	0.1725	2685	X-RAY DIFFRACTION	96
1.7875-1.8359	0.1996	123	0.1737	2714	X-RAY DIFFRACTION	96
1.8359-1.8899	0.2039	143	0.1948	2662	X-RAY DIFFRACTION	96
1.8899-1.9509	0.3203	122	0.255	2574	X-RAY DIFFRACTION	93
1.9509-2.0206	0.2109	152	0.1769	2733	X-RAY DIFFRACTION	97
2.0206-2.1015	0.2419	130	0.1911	2651	X-RAY DIFFRACTION	96
2.1015-2.1972	0.1963	144	0.1581	2706	X-RAY DIFFRACTION	97
2.1972-2.313	0.2323	148	0.1853	2693	X-RAY DIFFRACTION	96
2.313-2.4579	0.2022	163	0.1566	2730	X-RAY DIFFRACTION	98
2.4579-2.6476	0.2014	147	0.1583	2724	X-RAY DIFFRACTION	98
2.6476-2.9141	0.1735	145	0.1549	2734	X-RAY DIFFRACTION	98
2.9141-3.3356	0.1655	152	0.1502	2750	X-RAY DIFFRACTION	99
3.3356-4.2021	0.1544	133	0.1314	2790	X-RAY DIFFRACTION	99
4.2021-45.8	0.175	154	0.1477	2796	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	5.5016	0.5463	-3.8582	2.1553	-1.5286	7.5113	-0.0963	-0.298	-0.0764	-0.0629	-0.1352	-0.1168	0.2807	0.468	0.1458	0.0861	0.0222	-0.0241	0.1164	0.0102	0.1306	19.1148	18.2864	18.2442
2	0.7135	-0.8804	0.4698	2.3301	-2.2945	2.6334	0.1269	0.3451	-0.2446	-0.6912	-0.3751	-0.1729	0.5745	0.4135	0.2592	0.2905	0.0808	0.0546	0.2067	-0.0375	0.2192	20.1905	11.56	6.6822
3	5.2757	0.4581	-2.9682	3.3626	1.3618	2.4739	-0.6848	1.067	-0.527	-1.4475	0.0648	0.8466	-0.0288	-1.0843	0.5699	0.7534	-0.1201	-0.2163	0.4202	-0.127	0.5368	9.1729	0.8399	3.8539
4	3.5475	0.0956	-1.2018	3.637	-1.1037	4.8887	-0.1677	0.4214	-0.4357	-0.5374	0.2614	0.2296	0.4523	-0.3072	0.0204	0.1832	-0.0395	-0.0178	0.1683	-0.0471	0.1861	10.5755	9.5954	9.5458
5	8.3899	-2.0118	-5.0977	5.2475	0.9993	5.478	-0.1731	-0.4834	-0.5008	0.2422	-0.0023	-0.0362	0.1623	0.1828	0.1273	0.1226	-0.0012	-0.0326	0.1018	0.0293	0.1037	12.4493	9.7469	24.0648
6	9.6525	-1.9161	5.8153	3.8293	-3.4187	4.9942	0.1029	-2.7553	0.5329	1.3752	-0.3395	1.5372	-0.0797	-1.2743	0.2287	0.5063	-0.0205	0.1772	0.6548	-0.0883	0.6607	-1.9715	6.0956	28.4759
7	7.9025	5.0027	-0.4582	7.4366	0.4466	2.9489	0.1262	-0.4104	-0.0797	0.0515	-0.1379	-0.0542	-0.0245	0.0367	-0.0383	0.0813	0.0289	-0.0039	0.1207	-0.0127	0.0566	3.5407	21.6536	26.529
8	4.7908	1.135	-2.4262	1.8065	-0.0674	1.6803	-0.0257	0.074	0.0585	-0.1389	0.014	0.0976	-0.0549	-0.1429	-0.0044	0.1089	0.0006	-0.0457	0.1321	0.0101	0.0811	3.8765	23.931	18.2273
9	5.5833	-0.1765	2.0032	3.0724	1.2422	5.3097	0.0666	-0.1386	-0.1475	-0.0322	-0.1576	0.2141	-0.126	-0.4018	0.039	0.0883	0.0108	0.0147	0.1049	-0.0164	0.1348	2.083	37.7838	-3.9297
10	5.5502	-0.9323	1.8659	6.1165	-1.1951	1.5658	-0.0334	0.0877	0.0106	-0.5391	-0.0522	0.7408	-0.6977	-1.48	-0.0194	0.2303	0.0871	-0.0658	0.4142	-0.05	0.2034	-2.1499	33.2242	-18.6654
11	0.7065	-1.5529	0.0607	5.9461	3.4122	5.7009	0.4516	0.714	0.4936	-0.9652	-0.9169	-0.0857	-0.9414	-0.8603	0.2693	0.3214	0.109	-0.0475	0.3078	0.0714	0.2569	1.3974	45.4395	-18.1552
12	7.1015	6.897	-0.7106	7.6312	0.9463	6.0595	-0.4138	0.0758	0.5076	-0.6042	-0.1142	1.6269	-0.5311	-0.1522	0.3502	0.4326	-0.0109	0.0311	0.171	0.0565	0.6883	7.918	58.8726	-11.7812
13	6.4412	3.0613	2.1908	6.5133	5.0403	3.9198	-0.6407	1.2995	-0.0724	-1.3461	0.6372	0.5321	0.2944	-0.4108	-0.1976	1.0447	-0.3052	0.0907	0.3428	0.1087	0.3861	10.3033	54.2662	-21.9318
14	1.8548	1.1296	0.9003	2.034	0.4733	0.4433	0.0128	-0.008	0.1072	-0.1498	0.0212	0.1041	-0.0918	0.2608	0.0579	1.3263	-0.6737	-0.5751	1.3215	0.2406	0.6496	6.8917	43.0576	-29.205
15	4.9657	3.7028	3.6567	7.5629	2.8264	4.8259	-0.2825	0.6416	0.5991	-0.1856	0.2945	0.2599	-0.4083	0.467	-0.0255	0.1643	-0.0321	-0.005	0.147	0.0524	0.1776	11.6733	47.8968	-9.9433
16	4.1357	-0.6941	5.0556	3.3937	-0.5867	6.4321	-0.1958	-0.1923	0.6379	0.152	-0.0165	0.0288	-0.167	-0.02	0.2418	0.1291	-0.0106	0.02	0.1029	-0.0237	0.1666	9.3335	46.9528	1.2046
17	7.7535	-4.9384	-6.0252	8.875	4.3294	7.5607	-0.1769	-0.8629	0.7426	1.2739	-0.131	-0.3063	-0.9139	0.6154	0.2343	0.3093	-0.0561	-0.107	0.2524	-0.0551	0.2755	23.776	48.8267	4.3891
18	6.0363	3.796	-0.9889	6.8233	-0.1218	4.232	0.178	-0.2894	-0.0021	0.0048	-0.1215	-0.0075	-0.0039	0.0681	-0.0394	0.0776	0.023	-0.0146	0.0986	0.0192	0.0781	17.0695	33.7407	3.9572
19	3.5909	1.244	1.7925	2.0061	0.3124	1.2641	-0.0121	0.0944	-0.0768	-0.1798	0.0057	-0.0764	0.0724	0.1073	0.0052	0.1092	0.0016	0.0339	0.1394	-0.0078	0.0777	17.5083	32.6889	-4.6102

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 23 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 51 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 52 through 64 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 65 through 95 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 5 through 23 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 24 through 30 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 31 through 51 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 52 through 96 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 2 through 23 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 24 through 30 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 31 through 44 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 45 through 54 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 55 through 66 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 67 through 71 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 72 through 95 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 5 through 23 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 24 through 33 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 34 through 51 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 52 through 96 )

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