PDB-2egd: Crystal structure of human S100A13 in the Ca2+-bound state

ID or keywords:

Entry

Database: PDB / ID: 2egd

Title

Crystal structure of human S100A13 in the Ca2+-bound state

Components

Protein S100-A13

Keywords

METAL BINDING PROTEIN /

EF-HAND

Function / homology

Function and homology information

positive regulation of interleukin-1 alpha production /

RAGE receptor binding / mast cell degranulation /

fibroblast growth factor binding / positive regulation of cytokine production / calcium-dependent protein binding /

protein transport / positive regulation of canonical NF-kappaB signal transduction / copper ion binding /

lipid binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Imai, F.L. / Nagata, K. / Yonezawa, N. / Nakano, M. / Tanokura, M.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Crystal structure of human S100A13 in the Ca2+-bound state
Authors: Imai, F.L. / Nagata, K. / Yonezawa, N. / Nakano, M. / Tanokura, M.

History

Deposition	Feb 28, 2007	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 11, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Derived calculations / Version format compliance
Revision 1.2	Oct 25, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2egd.cif.gz	52.6 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	2egd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eg/2egd ftp://data.pdbj.org/pub/pdb/validation_reports/eg/2egd	HTTPS FTP

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Related structure data

Related structure data	1xk4S S: Starting model for refinement
Similar structure data	3iwy-d 3upc-12 6wn7-3 5cd7-1 3lwk-d 2o2v-d 4mjs-4 3lnj-2 1e8a-d 5v8w-3 Search similar-shape structures by Omokage search (details) 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-A13

B: Protein S100-A13

hetero molecules

23.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	39.774, 59.287, 77.624
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Protein S100-A13 / S100 calcium-binding protein A13 Mass: 11490.193 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: S100A13 / Plasmid: pET-16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99584
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.99 Å³/Da / Density % sol: 38.22 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 22% PEG 3350, 0.1M HEPES-NaOH (pH 7.5), 0.2M NaCl, 1.5% 1,2,3-heptanetriol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2006 Details: Rotated-inclined double-crystal monochromator, rhodium-coated horizontal mirror
Radiation	Monochromator: Rotated-inclined double-crystal monochromator, rhodium-coated horizontal mirror. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. obs: 17786 / % possible obs: 99.1 % / Observed criterion σ(I): 3.4 / Redundancy: 6.9 % / R_sym value: 0.066 / Net I/σ(I): 31.5
Reflection shell	Resolution: 1.8→1.86 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 3.4 / R_sym value: 0.335 / % possible all: 93

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
BSS	(Beamline Scheduling Software)	data collection
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XK4

1xk4

Resolution: 1.8→47.14 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.936 / SU B: 4.972 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23418	897	5.1 %	RANDOM
R_work	0.19541	-	-	-
obs	0.19732	16683	99.17 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 24.001 Å²

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 1.8→47.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1383	0	4	34	1421

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	1402
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.467	1.97	1889
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.232	5	175
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.698	26	60
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.271	15	266
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.278	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.114	0.2	225
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1006
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	697
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.308	0.2	1017
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	55
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.083	0.2	18
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.152	0.2	24
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.213	0.2	4
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.859	1.5	908
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.146	2	1417
X-RAY DIFFRACTION	r_scbond_it	2.064	3	557
X-RAY DIFFRACTION	r_scangle_it	2.993	4.5	472
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.796→1.843 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.285	70	-
R_work	0.199	1104	-
obs	-	-	91.86 %

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	13.5354	-5.1445	-1.0347	15.4706	-0.6714	16.2972	-0.0042	-0.4481	-0.9898	0.3264	-0.0069	0.4419	1.1835	-0.5576	0.0111	0.0652	-0.0444	-0.0397	-0.0973	0.0512	-0.0229	2.065	5.358	22.426
2	14.8943	2.0836	1.5998	14.3891	9.4314	21.5151	-0.0283	-0.5341	-0.9364	0.4597	-0.0274	0.1694	0.8533	-0.4416	0.0557	-0.0789	0.0091	0.0134	-0.1179	0.054	-0.0443	5.761	10.717	26.743
3	1.297	0.235	2.5357	5.0007	9.0835	19.958	0.0317	-0.339	0.0433	0.1976	0.0612	0.0117	0.3525	-0.4845	-0.0929	-0.0989	-0.0077	0.0184	-0.0739	0.0417	-0.0759	6.215	17.505	33.565
4	10.3307	-8.5828	-0.5563	15.6477	13.5489	20.1381	0.3422	-1.144	-0.2806	0.6921	-0.5166	0.2123	0.7589	-0.2403	0.1744	-0.0347	-0.045	0.0203	-0.0435	0.0585	-0.0772	9.045	17.645	40.442
5	12.0343	8.2367	13.477	14.9141	-2.4969	44.4079	0.2284	-1.0756	0.381	0.8616	-0.135	0.911	-0.8351	-0.4725	-0.0933	-0.0396	-0.0073	0.0665	0.0141	-0.0752	-0.0178	5.813	24.73	41.631
6	17.4047	0.0592	-2.6239	8.9339	-4.1428	2.956	0.3544	-0.6499	0.6191	0.3905	-0.4259	-0.3347	-0.29	0.3943	0.0715	-0.0589	-0.0394	0.0112	-0.0716	-0.0192	-0.0757	14.348	25.01	38.649
7	9.3969	-10.3631	-5.9855	17.7217	1.6512	7.7055	-0.0077	-0.7795	-0.0647	0.5381	0.3716	-0.7176	0.2357	1.0499	-0.3639	-0.0894	0.0065	-0.0494	0.0514	-0.0072	-0.0691	18.81	20.069	36.356
8	8.2763	3.3484	-6.2774	7.5065	-1.577	14.3272	-0.2632	0.1454	-0.3347	-0.2916	0.0383	-0.6993	0.4842	0.6734	0.2249	-0.0652	0.0621	-0.0152	0.001	0.0053	-0.0311	20.355	15.833	29.874
9	8.1558	-10.3344	-2.1362	34.6688	12.2203	4.7547	0.2148	-0.4811	0.4643	-0.6731	0.6413	-1.4517	-0.0595	0.9735	-0.8561	-0.0058	-0.0381	0.0425	0.1128	-0.0968	0.1686	24.662	25.494	30.12
10	23.2344	-2.917	10.1728	10.9443	0.8308	12.0907	0.0524	0.1062	0.9236	-0.518	0.0249	-0.491	-0.7946	0.7736	-0.0774	0.0042	-0.0559	0.0257	-0.104	-0.0729	0.0356	17.638	31.124	30.898
11	9.1881	-2.9734	-7.608	17.6576	6.65	31.8885	0.4046	0.4666	0.3248	-0.7515	-0.2825	0.6168	-2.0698	-0.771	-0.122	0.085	0.0746	-0.0663	-0.1115	-0.038	0.0499	9.413	35.559	32.462
12	25.6974	26.0328	16.2842	36.5615	11.3748	12.894	0.0428	-0.8939	0.5747	0.616	-0.7781	0.4007	-0.2307	-1.0193	0.7352	-0.112	0.0382	-0.012	-0.1084	-0.0346	-0.0551	7.51	27.944	34.336
13	2.1363	4.3856	0.5129	11.8981	-2.9986	5.7935	-0.3501	0.0464	0.1122	-0.165	0.1339	0.6112	-0.235	0.0131	0.2162	-0.0987	-0.0021	-0.0239	-0.1088	-0.0211	-0.0671	7.532	24.356	27.61
14	18.0347	-10.1781	-9.4114	14.9725	19.8334	27.7635	-0.3933	0.2636	0.6833	-0.0572	0.5927	-0.6452	-0.4296	1.1556	-0.1994	-0.0776	-0.0433	-0.0175	-0.0837	-0.0002	-0.0661	13.577	22.984	23.454
15	35.1854	4.4448	-21.6097	17.8203	7.1063	42.8436	0.0578	1.7872	0.0854	-0.9432	0.3596	-1.1948	-0.2013	0.5789	-0.4174	-0.006	-0.0829	0.0254	0.1984	-0.0586	-0.0112	17.077	18.764	15.272
16	11.2038	-0.6615	8.9732	8.08	5.3178	19.3238	0.2092	-0.068	-0.8392	0.2398	0.3851	-0.4413	1.1233	0.6259	-0.5943	-0.0432	0.0509	-0.0333	-0.0613	-0.0306	-0.0035	16.058	10.54	26.988
17	6.3055	-0.6324	4.1401	0.0913	0.4591	30.1757	-0.1875	0.7031	-0.2281	0.0931	0.4286	-0.1872	0.0779	0.674	-0.2411	-0.0797	0.0293	-0.0248	-0.0979	-0.0234	-0.0557	12.25	11.825	18.952
18	0.8573	-0.1008	2.8786	4.7727	2.2363	11.0576	0.0399	0.1877	-0.3797	-0.1163	0.1724	-0.4029	-0.0481	0.3663	-0.2123	-0.0565	-0.0191	0.0176	-0.0414	-0.0383	-0.0403	9.046	10.264	10.04
19	20.1861	-8.3477	-2.1853	14.3329	4.2241	40.0897	-0.2637	0.0063	-0.4115	-1.0069	0.2236	-0.0711	0.4241	-0.1262	0.04	-0.0358	-0.0347	0.0281	-0.0169	-0.0625	-0.0641	8.884	10.336	1.665
20	24.8688	-0.5302	-6.0887	8.1668	-1.5031	8.7157	-0.1472	0.8777	0.5518	-0.3511	0.3532	-0.2695	-0.2629	0.5366	-0.206	0.0031	-0.077	0.0226	-0.0667	-0.0252	-0.0861	6.442	14.21	3.908
21	13.1619	1.0938	-4.5537	10.4221	-1.0586	10.1574	0.0953	0.5103	-0.34	-0.108	0.1586	0.3156	0.1633	-0.2212	-0.2539	-0.0893	-0.0522	-0.0283	-0.0882	-0.0058	-0.0572	0.01	9.793	6.962
22	6.1259	0.2915	5.5346	11.5093	1.454	14.0777	0.0184	-0.0471	-0.4621	0.1051	0.2811	0.2771	0.6145	-0.5564	-0.2995	-0.0244	-0.0785	-0.0386	-0.1038	0.0343	-0.0128	-0.904	6.366	14.708
23	17.8137	-3.3364	3.4564	6.2835	-7.0053	24.3218	-0.2442	-0.4465	0.0823	-0.1167	0.2832	0.5906	0.1308	-2.0419	-0.039	0.0047	-0.098	0.0117	0.0898	-0.0121	0.1193	-6.764	10.566	18.876
24	13.8237	7.7836	10.3765	28.9953	9.8108	25.67	0.011	-0.8049	-0.1651	-0.2209	-0.3751	1.2725	-0.2604	-1.9796	0.3642	-0.0292	0.0003	-0.0469	0.0747	-0.0062	0.038	-8.485	15.864	8.563
25	13.0382	5.0622	-2.7372	9.6872	2.5278	14.2234	-0.1338	0.1642	0.436	-0.8025	0.098	0.377	-1.1048	-0.4591	0.0358	0.1481	0.0167	-0.0578	-0.0879	0.049	-0.0526	-0.803	22.991	5.699
26	17.9851	-4.6817	9.449	12.2979	0.7839	6.8645	-0.0296	0.7415	0.17	-0.8877	-0.0474	-0.0169	0.1523	1.0499	0.077	0.0006	-0.1049	0.036	-0.0777	0.0373	-0.0889	5.815	19.014	6.426
27	5.2214	0.8826	1.0769	8.6292	0.3752	9.5379	-0.14	-0.0671	0.2322	-0.3	-0.1479	-0.3775	-0.5631	0.5136	0.2879	-0.0534	-0.0373	-0.0021	-0.1022	0.001	-0.0899	6.199	19.944	13.871
28	4.8916	2.0225	-11.3773	1.8041	-0.9643	40.9117	-0.1046	-0.0222	0.1112	-0.0508	-0.0569	0.5124	-0.5663	-1.0567	0.1615	-0.0695	-0.0003	-0.0292	-0.1056	-0.001	-0.0796	0.389	18.788	20.366
29	17.3119	10.1285	-2.7101	5.972	-0.3106	35.5809	0.1835	0.0055	1.0693	-0.3131	-0.0864	0.7389	-0.5507	-1.4041	-0.0971	-0.0725	0.0697	0.0139	-0.0373	0.002	0.007	-2.943	18.024	29.532
30	34.3143	-0.9131	-8.0372	3.7186	-3.8489	19.308	-0.0529	-0.2126	1.8379	0.4208	0.7187	0.142	-0.6492	-1.6931	-0.6658	0.1216	0.0015	0.0438	0.0893	0.0544	0.0507	-7.082	19.37	37.922

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	5 - 10	5 - 10
2	X-RAY DIFFRACTION	2	A	A	11 - 16	11 - 16
3	X-RAY DIFFRACTION	3	A	A	17 - 21	17 - 21
4	X-RAY DIFFRACTION	4	A	A	22 - 26	22 - 26
5	X-RAY DIFFRACTION	5	A	A	27 - 32	27 - 32
6	X-RAY DIFFRACTION	6	A	A	33 - 38	33 - 38
7	X-RAY DIFFRACTION	7	A	A	39 - 43	39 - 43
8	X-RAY DIFFRACTION	8	A	A	44 - 50	44 - 50
9	X-RAY DIFFRACTION	9	A	A	51 - 57	51 - 57
10	X-RAY DIFFRACTION	10	A	A	58 - 63	58 - 63
11	X-RAY DIFFRACTION	11	A	A	64 - 68	64 - 68
12	X-RAY DIFFRACTION	12	A	A	69 - 73	69 - 73
13	X-RAY DIFFRACTION	13	A	A	74 - 77	74 - 77
14	X-RAY DIFFRACTION	14	A	A	78 - 83	78 - 83
15	X-RAY DIFFRACTION	15	A	A	84 - 90	84 - 90
16	X-RAY DIFFRACTION	16	B	B	6 - 12	6 - 12
17	X-RAY DIFFRACTION	17	B	B	13 - 18	13 - 18
18	X-RAY DIFFRACTION	18	B	B	19 - 24	19 - 24
19	X-RAY DIFFRACTION	19	B	B	25 - 29	25 - 29
20	X-RAY DIFFRACTION	20	B	B	30 - 35	30 - 35
21	X-RAY DIFFRACTION	21	B	B	36 - 41	36 - 41
22	X-RAY DIFFRACTION	22	B	B	42 - 47	42 - 47
23	X-RAY DIFFRACTION	23	B	B	48 - 53	48 - 53
24	X-RAY DIFFRACTION	24	B	B	54 - 59	54 - 59
25	X-RAY DIFFRACTION	25	B	B	60 - 68	60 - 68
26	X-RAY DIFFRACTION	26	B	B	69 - 73	69 - 73
27	X-RAY DIFFRACTION	27	B	B	74 - 77	74 - 77
28	X-RAY DIFFRACTION	28	B	B	78 - 85	78 - 85
29	X-RAY DIFFRACTION	29	B	B	86 - 90	86 - 90
30	X-RAY DIFFRACTION	30	B	B	91 - 96	91 - 96

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