PDB-6gkt: X-ray structure of a non-autocrystallizing galectin-10 variant, G...

ID or keywords:

Entry

Database: PDB / ID: 6gkt

Title

X-ray structure of a non-autocrystallizing galectin-10 variant, Gal10-Tyr69Glu

Components

Galectin-10

Keywords

SUGAR BINDING PROTEIN / Non-autocrystallizing / mutant / galectin-10

Function / homology

Function and homology information

regulation of activated T cell proliferation / regulation of T cell cytokine production / T cell apoptotic process / regulation of T cell anergy / : / carbohydrate binding / identical protein binding / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Verstraete, K. / Verschueren, K. / Savvides, S.N.

Funding support

Belgium, 1items

Citation

Journal: Science / Year: 2019
Title: Protein crystallization promotes type 2 immunity and is reversible by antibody treatment.
Authors: Emma K Persson / Kenneth Verstraete / Ines Heyndrickx / Elien Gevaert / Helena Aegerter / Jean-Michel Percier / Kim Deswarte / Koen H G Verschueren / Ann Dansercoer / Delphine Gras / Pascal ...
Abstract: Although spontaneous protein crystallization is a rare event in vivo, Charcot-Leyden crystals (CLCs) consisting of galectin-10 (Gal10) protein are frequently observed in eosinophilic diseases, such ...

History

Deposition	May 21, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 5, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6gkt.cif.gz	368.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6gkt.ent.gz	304.2 KB	Display	PDB format
PDBx/mmJSON format	6gkt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gk/6gkt ftp://data.pdbj.org/pub/pdb/validation_reports/gk/6gkt	HTTPS FTP

-
Related structure data

Related structure data	SASDF86C 6gkqC 6gksC 6gkuC 6glwC 6glxC 6qrnC 1lclS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3gae-2 3c85-2 6m26-d 6l68-1 4yn9-d 3m54-d 3t7g-2 4jlg-1 6m28-d 6m27-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Galectin-10

B: Galectin-10

C: Galectin-10

D: Galectin-10

E: Galectin-10

F: Galectin-10

hetero molecules

101 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Galectin-10

B: Galectin-10

hetero molecules

defined by author
Evidence: SAXS, light scattering
33.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Galectin-10

D: Galectin-10

hetero molecules

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

3

E: Galectin-10

F: Galectin-10

hetero molecules

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

Unit cell

Length a, b, c (Å)	72.823, 93.296, 93.068
Angle α, β, γ (deg.)	90.00, 108.94, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Galectin-10 / Gal-10 / Charcot-Leyden crystal protein / CLC / Eosinophil lysophospholipase / Lysolecithin acylhydrolase Mass: 16632.971 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: Recombinant human galectin-10-Tyr69Glu was produced with an N-terminal cleavable His-tag (MASTTHHHHHHDTDIPTTGGGSRPDDDDKENLYFQG). The His-tag was removed by TEV-cleavage before crystallization. Source: (gene. exp.) Homo sapiens (human) / Gene: CLC, LGALS10, LGALS10A / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05315
#2: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#3: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#4: Chemical	ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₇ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 645 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3 Å³/Da / Density % sol: 58.95 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium citrate pH 5.1 20% PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99998 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 68207 / % possible obs: 99 % / Redundancy: 6.9 % / B_iso Wilson estimate: 39.7 Å² / CC_1/2: 0.99 / R_rim(I) all: 0.15 / Net I/σ(I): 9.33
Reflection shell	Resolution: 2.1→2.23 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 10924 / CC_1/2: 0.36 / R_rim(I) all: 2.27 / % possible all: 98.6

-
Processing

Software

Name	Version	Classification
BUSTER	2.10.2	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1LCL

1lcl

Resolution: 2.1→42 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.947 / R_factor R_free error: 0 / SU R Cruickshank DPI: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.166 / SU R_free Blow DPI: 0.144 / SU R_free Cruickshank DPI: 0.142

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.204	3368	4.94 %	RANDOM
R_work	0.172	-	-	-
obs	0.174	68187	99.1 %	-

Displacement parameters

B_iso mean: 51.83 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-8.5691 Å²	0 Å²	-0.7405 Å²
2-	-	5.0708 Å²	0 Å²
3-	-	-	3.4983 Å²

Refine analyze

Luzzati coordinate error obs: 0.26 Å

Refinement step

Cycle: 1 / Resolution: 2.1→42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6766	0	112	648	7526

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	7029	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.12	9460	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		2509	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		186	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		979	HARMONIC	5
X-RAY DIFFRACTION	t_it		7029	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	4.03
X-RAY DIFFRACTION	t_other_torsion	17.9
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		871	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		7608	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.1→2.15 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.232	237	4.7 %
R_work	0.217	4804	-
all	0.218	5041	-
obs	-	-	99.12 %

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	2.3312	-0.2063	-0.7339	1.414	0.0914	3.3036	-0.0416	-0.2174	0.0536	0.1928	-0.043	-0.1077	0.2285	0.454	0.0845	0.0332	0.0775	-0.0473	-0.0468	0.0319	0.0048	3.9916	11.8364	46.0434
2	1.7814	-0.0567	0.9371	0.7425	-0.4655	2.0055	-0.0649	-0.0252	-0.0862	-0.3818	0.0705	-0.0859	0.2543	-0.0725	-0.0056	0.056	0.0017	0.0231	-0.0805	-0.0066	-0.0243	-4.6323	7.2583	34.4094
3	2.2973	0.284	1.1113	2.3693	-1.1732	4.2988	-0.0475	-0.1811	0.0605	0.3391	0.1318	-0.1561	-0.1121	-0.0655	-0.0843	0.0098	0.0284	-0.0174	-0.0666	0.0009	0.0136	-4.8199	19.0687	44.6524
4	1.115	0.6243	1.0989	3.1614	0.9541	3.1276	-0.1214	0.0939	0.1656	0.0818	-0.0418	0.1595	-0.1813	-0.3375	0.1632	0.0395	0.0296	0.0028	-0.0085	0.0099	0.0027	-10.0297	23.3159	38.6966
5	2.8361	2.0268	1.5221	0	-2.2729	4.1148	-0.1147	0.2273	0.006	-0.2324	-0.0253	0.0442	0.0835	-0.0984	0.14	-0.0001	-0.0253	0.0473	-0.0544	0.0031	-0.0731	-6.2309	12.9183	27.3259
6	0.7874	-1.3651	-1.1403	0.1442	-0.7668	1.5402	-0.0347	0.2646	0.1227	-0.1059	-0.0442	-0.214	0.0592	0.3237	0.0789	0.034	0.0075	0.0276	0.0062	0.0371	0.0525	4.7029	17.8735	33.0724
7	0.9643	0.1032	-0.1992	1.8801	-0.0254	1.8656	-0.0787	0.0321	0.1914	0.0058	0.0715	-0.2221	-0.2393	-0.0048	0.0072	0.0066	0.0252	-0.0103	-0.0791	-0.0036	0.0164	-0.1782	21.2682	40.3176
8	1.2888	-1.6365	-0.8008	0.3983	-1.2023	1.69	-0.1201	0.0939	0.1947	-0.0238	0.029	-0.3618	0.1612	0.2135	0.0911	-0.0197	0.0308	-0.0394	-0.1182	0.0308	0.0756	8.4148	12.0948	40.4876
9	0.3972	0.7713	-0.9975	2.3386	0.451	3.5824	-0.0845	-0.0789	-0.2015	-0.1244	0.0159	0.2616	0.1146	0.2637	0.0686	-0.0677	0.0136	0.0077	-0.2086	0.0629	-0.0572	-20.677	-6.636	44.4911
10	0.1007	-0.2388	0.2743	2.182	0.4347	0.606	-0.0613	-0.2589	0.038	0.0654	-0.0771	0.1197	-0.1518	-0.0865	0.1383	0.0757	0.0143	0.0398	-0.059	0.0292	-0.0287	-18.7824	7.1726	50.369
11	2.347	0.2377	-1.5356	4.0702	0.0922	3.8469	-0.1436	0.3545	-0.0658	-0.4269	0.1821	0.2935	-0.0335	-0.1791	-0.0385	0.0753	-0.0373	-0.0256	-0.0612	0.0582	0.0027	-22.8297	1.2547	36.4582
12	2.7722	0.2985	0.3666	0.7809	-1.2371	2.5476	-0.1325	0.0221	0.4667	-0.1218	0.0781	0.5325	-0.2906	-0.2188	0.0544	0.0384	0.0115	-0.0464	-0.1625	0.0813	0.0493	-26.2894	10.9445	40.6374
13	3.0279	-0.1076	-0.7975	1.7331	-1.6563	-0.9017	0.0697	-0.1666	-0.0868	0.295	0.0288	0.6309	-0.0092	-0.1085	-0.0986	-0.0298	0.0177	0.0445	-0.1067	0.0628	0.0889	-31.7603	1.5214	48.4202
14	0.9135	1.032	-0.4447	1.5205	-0.3134	1.5714	-0.114	0.1538	0.2282	-0.32	0.1981	0.4651	-0.1396	-0.1272	-0.0841	0.0159	-0.0058	-0.0352	-0.1022	0.0576	0.0602	-28.651	0.6641	39.6204
15	0.3006	1.186	-0.1383	1.8435	0.9128	-0.1303	-0.0257	-0.1546	-0.0533	0.2912	-0.0884	0.2844	-0.0872	0.0433	0.1141	-0.0216	0.0059	0.0509	-0.0052	0.0387	0.0349	-25.6739	-6.4128	49.7218
16	3.9195	1.0797	0.3544	3.3591	1.4911	4.2977	0.1241	-0.0964	0.2987	-0.5006	-0.1015	0.0353	-0.469	0.5284	-0.0226	0.0002	-0.0183	0.0408	-0.0266	0.0501	-0.1555	-30.4578	11.5366	72.717
17	6.923	0.7986	-1.797	2.2279	0.2548	2.5826	0.0099	-0.1978	-0.1416	-0.1064	-0.0418	-0.0742	0.0439	0.4658	0.0319	-0.0256	0.0212	-0.0048	0.0507	0.0107	-0.0926	-31.1622	2.6569	79.0628
18	-0.1191	-0.5412	1.975	2.3804	-1.6589	1.5141	0.0395	-0.0167	-0.1902	0.0507	0.0411	-0.0534	0.1146	0.059	-0.0806	0.0348	0.0398	0.0388	0.0289	0.0559	0.0125	-33.2094	-6.5609	83.7288
19	3.4852	-1.5326	1.2557	1.1522	-0.4194	1.5974	0.1505	0.026	-0.2009	0.0324	0.082	-0.1532	-0.1985	0.3603	-0.2324	-0.0594	-0.0401	0.0799	0.1684	0.0044	-0.1661	-17.1175	6.6422	74.514
20	0.783	1.5925	-0.2233	2.1356	-0.5076	3.8742	0.0563	0.383	-0.1653	-0.2656	0.0142	0.1213	0.1275	0.4782	-0.0704	0.0298	0.0809	0.0489	0.1189	-0.0111	-0.0621	-26.5569	2.2241	66.0022
21	0.0134	0.5636	0.2976	1.0861	-0.6777	2.4517	0.1086	-0.0375	-0.3195	-0.3562	-0.0589	-0.0999	0.3379	0.4592	-0.0497	-0.0257	0.0683	-0.005	-0.0094	-0.0282	-0.0339	-32.2066	-0.2601	73.166
22	1.244	-2.4793	0.105	0.5077	-0.4143	0.9872	0.0849	0.0912	0.0196	-0.137	-0.0385	-0.0019	-0.1963	0.1358	-0.0464	0.0238	-0.0199	0.0205	0.0072	0.0179	-0.115	-34.5351	11.4673	67.039
23	2.6764	0.7441	-1.3208	2.1981	1.7332	3.4774	0.0409	0.1647	0.192	-0.2272	-0.0854	-0.1319	-0.3707	-0.071	0.0445	0.2355	-0.1801	-0.0789	-0.1501	0.0567	-0.0567	-27.0498	28.2339	92.5538
24	-0.4929	1.1926	0.2978	3.2878	0.5176	2.4504	-0.0666	0.0282	0.1397	-0.0468	-0.0613	0.2299	-0.1174	0.0592	0.1279	-0.0825	-0.0211	-0.041	-0.0731	-0.0578	0.0334	-34.5223	14.9934	93.046
25	-0.0798	-1.2036	0.1878	2.37	0.9354	3.7182	0.0348	0.3382	0.0058	-0.3785	0.0088	-0.004	-0.4178	0.6911	-0.0437	-0.0245	-0.1527	0.0451	0.1346	-0.0232	-0.0933	-19.5322	19.5991	92.2665
26	3.3444	1.5193	3.2289	2.7971	1.5107	4.523	0.0513	0.2859	-0.4488	0.0926	0.1711	-0.4119	0.3096	0.6735	-0.2225	-0.1194	0.0249	0.0153	0.0237	-0.032	-0.0267	-23.3305	10.3475	97.142
27	-0.1081	1.0806	-0.4442	0.8768	0.7952	4.9427	0.0656	-0.1689	0.0079	0.0145	-0.264	0.1154	-0.2914	0.3362	0.1984	0.0144	-0.0478	-0.0008	-0.0468	-0.0098	-0.0246	-27.8697	20.3399	104.4945
28	1.6945	0.6749	0.4654	2.9155	0.667	2.2986	-0.1521	0.0677	-0.0603	-0.1191	0.0624	-0.4046	-0.1601	0.5986	0.0898	-0.047	-0.0867	0.0335	0.0534	0	-0.0352	-20.6137	20.4739	98.8427
29	1.7222	1.3495	-0.4802	1.9725	0.3826	0.1828	0.1192	0.055	0.1189	0.0121	-0.206	0.0658	-0.2678	0.054	0.0868	0.1192	-0.0917	-0.0749	-0.1303	0.0269	-0.0311	-30.7741	28.2684	99.1114
30	4.8122	-0.1534	0.2434	2.4819	-1.0545	2.5659	-0.0276	-0.5209	-0.0669	-0.0258	0.1222	0.198	0.2699	-0.1587	-0.0946	0.0321	-0.0659	0.0166	0.0271	0.1253	-0.0449	-0.5866	-1.9739	73.9842
31	2.0179	-2.8677	1.7924	0.4856	0.3689	2.5378	-0.0959	-0.3478	0.2444	0.0654	-0.0775	0.0647	-0.1587	-0.4629	0.1734	-0.0664	0.0902	-0.0272	-0.0451	-0.0094	-0.1056	0.5276	11.0765	65.8986
32	6.3077	-0.9709	2.3309	1.9845	0.3289	4.5558	0.1222	-0.4073	-0.391	0.1708	0.0235	-0.0873	0.4076	-0.0203	-0.1457	0.0249	0.0306	-0.0873	-0.0867	0.0687	0.0138	9.4541	-1.5847	68.4697
33	-0.0224	2.6883	-0.5591	0.7412	-0.8929	3.4487	0.0041	0.115	0.0328	-0.0453	0.0058	-0.1756	-0.081	-0.0254	-0.0099	0.0089	0.039	-0.0578	-0.0755	0.0362	0.0741	8.8853	7.8604	58.4334
34	3.3878	-3.291	-1.5836	0.5502	0.7334	-1.3599	0.0414	-0.0474	-0.1713	-0.0569	-0.0307	-0.2241	0.0585	0.1377	-0.0107	0.0853	0.1073	-0.118	-0.0549	-0.0162	0.126	17.5079	-4.856	62.6426
35	1.1839	-0.5331	2.378	2.7358	-3.1634	3.9715	-0.0389	0.0097	0.0937	-0.1558	0.0209	-0.1312	0.0521	-0.293	0.0179	0.008	0.0134	-0.0709	-0.129	-0.029	-0.0391	2.1712	10.6152	56.5707
36	3.8586	2.0458	2.4098	0.5119	-0.1425	2.5839	0.037	-0.1826	-0.1138	-0.0176	0.1685	0.2814	0.3473	-0.3795	-0.2055	0.0486	-0.0257	-0.0674	-0.0343	0.0651	0.0016	-2.7242	-1.4665	59.7441
37	2.4888	1.4257	0.4394	0.6004	-2.0704	0.895	-0.0317	0.041	-0.5488	-0.045	0.0128	-0.1381	0.4977	-0.0452	0.0189	0.1766	0.068	-0.1169	-0.2117	-0.0032	-0.0124	4.4883	-7.5773	60.0653
38	-1.3856	-1.0741	1.7082	0	0.1963	2.7973	-0.0219	-0.3038	-0.0675	0.0665	-0.0348	0.0676	0.1105	-0.0453	0.0568	-0.0313	0.013	-0.0528	-0.0249	0.0595	0.0243	6.6664	3.101	71.8158
39	2.1098	0.7545	-0.3307	1.1103	1.0088	1.8198	-0.1021	-0.3678	0.0405	-0.0255	0.2189	0.1825	0.1567	-0.499	-0.1168	0.0041	-0.0124	-0.0309	0.0586	0.0991	-0.0457	-6.8717	-1.3252	69.1582
40	4.3901	-2.3643	-1.6301	1.7774	2.2657	4.243	-0.0237	-0.5049	0.5196	0.2246	-0.0392	-0.0023	-0.4501	-0.0916	0.0629	-0.0259	0.0743	-0.1063	-0.0614	-0.1352	0.0209	13.2394	23.8457	81.8504
41	3.6701	-1.4433	0.5927	5.6115	-0.2117	1.5186	-0.0035	-0.1186	0.5187	-0.3611	-0.1631	0.3174	-0.2656	-0.1198	0.1666	0.0105	0.0991	-0.1089	-0.1616	-0.0533	0.0181	15.7396	18.942	70.3828
42	1.4968	-0.7923	0.3788	5.4021	0.0433	2.7137	0.0436	-0.0397	0.6188	-0.5168	0.1056	0.0667	-0.4567	-0.1903	-0.1493	-0.0681	0.0362	-0.0456	-0.1593	0.0439	0.0623	21.5821	19.21	68.0084
43	0.5828	1.3	1.4144	2.6278	3.3702	0.9021	-0.1535	-0.4832	0.5067	0.076	0.0393	-0.2326	-0.0833	0.2051	0.1142	-0.0626	0.0232	-0.0628	-0.0655	-0.1527	0.1947	24.8223	24.5402	79.4815
44	0.9844	-0.7372	-0.1035	0.4579	1.1594	2.7754	0.0534	-0.2835	0.5377	-0.2099	-0.1361	-0.2657	-0.5144	0.0516	0.0826	-0.0138	0.0601	-0.1108	-0.2629	-0.0747	0.2055	18.8975	27.1078	72.6318
45	-0.4033	-1.5578	0.5185	0.1952	0.2971	0.4033	-0.0319	-0.2361	0.1706	0.0161	0.0418	-0.0387	-0.0374	-0.0548	-0.0098	-0.0328	0.0463	-0.0127	-0.0102	-0.1448	0.0418	13.5619	21.8815	84.5403

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|2 - A\|17 }
2	X-RAY DIFFRACTION	2	{ A\|18 - A\|34 }
3	X-RAY DIFFRACTION	3	{ A\|35 - A\|57 }
4	X-RAY DIFFRACTION	4	{ A\|58 - A\|75 }
5	X-RAY DIFFRACTION	5	{ A\|76 - A\|87 }
6	X-RAY DIFFRACTION	6	{ A\|88 - A\|106 }
7	X-RAY DIFFRACTION	7	{ A\|107 - A\|129 }
8	X-RAY DIFFRACTION	8	{ A\|130 - A\|141 }
9	X-RAY DIFFRACTION	9	{ B\|2 - B\|17 }
10	X-RAY DIFFRACTION	10	{ B\|18 - B\|34 }
11	X-RAY DIFFRACTION	11	{ B\|35 - B\|57 }
12	X-RAY DIFFRACTION	12	{ B\|58 - B\|87 }
13	X-RAY DIFFRACTION	13	{ B\|88 - B\|106 }
14	X-RAY DIFFRACTION	14	{ B\|107 - B\|129 }
15	X-RAY DIFFRACTION	15	{ B\|130 - B\|141 }
16	X-RAY DIFFRACTION	16	{ C\|2 - C\|34 }
17	X-RAY DIFFRACTION	17	{ C\|35 - C\|65 }
18	X-RAY DIFFRACTION	18	{ C\|66 - C\|75 }
19	X-RAY DIFFRACTION	19	{ C\|76 - C\|87 }
20	X-RAY DIFFRACTION	20	{ C\|88 - C\|106 }
21	X-RAY DIFFRACTION	21	{ C\|107 - C\|129 }
22	X-RAY DIFFRACTION	22	{ C\|130 - C\|139 }
23	X-RAY DIFFRACTION	23	{ D\|2 - D\|17 }
24	X-RAY DIFFRACTION	24	{ D\|18 - D\|34 }
25	X-RAY DIFFRACTION	25	{ D\|35 - D\|57 }
26	X-RAY DIFFRACTION	26	{ D\|58 - D\|87 }
27	X-RAY DIFFRACTION	27	{ D\|88 - D\|106 }
28	X-RAY DIFFRACTION	28	{ D\|107 - D\|129 }
29	X-RAY DIFFRACTION	29	{ D\|130 - D\|141 }
30	X-RAY DIFFRACTION	30	{ E\|2 - E\|17 }
31	X-RAY DIFFRACTION	31	{ E\|18 - E\|34 }
32	X-RAY DIFFRACTION	32	{ E\|35 - E\|57 }
33	X-RAY DIFFRACTION	33	{ E\|58 - E\|65 }
34	X-RAY DIFFRACTION	34	{ E\|66 - E\|75 }
35	X-RAY DIFFRACTION	35	{ E\|76 - E\|87 }
36	X-RAY DIFFRACTION	36	{ E\|88 - E\|106 }
37	X-RAY DIFFRACTION	37	{ E\|107 - E\|122 }
38	X-RAY DIFFRACTION	38	{ E\|123 - E\|129 }
39	X-RAY DIFFRACTION	39	{ E\|130 - E\|141 }
40	X-RAY DIFFRACTION	40	{ F\|2 - F\|26 }
41	X-RAY DIFFRACTION	41	{ F\|27 - F\|65 }
42	X-RAY DIFFRACTION	42	{ F\|66 - F\|87 }
43	X-RAY DIFFRACTION	43	{ F\|88 - F\|106 }
44	X-RAY DIFFRACTION	44	{ F\|107 - F\|129 }
45	X-RAY DIFFRACTION	45	{ F\|130 - F\|138 }

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi