PDB-3tdo: Crystal structure of HSC at pH 9.0

ID or keywords:

Entry

Database: PDB / ID: 3tdo

Title

Crystal structure of HSC at pH 9.0

Components

Putative formate/nitrite transporter

Keywords

MEMBRANE PROTEIN

Function / homology

Function and homology information

transmembrane transporter activity / membrane / metal ion binding
Similarity search - Function

Biological species

Peptoclostridium difficile (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.197 Å

Authors

Czyzewski, B.K. / Wang, D.-N.

Citation

Journal: Nature / Year: 2012
Title: Identification and characterization of a bacterial hydrosulphide ion channel.
Authors: Czyzewski, B.K. / Wang, D.N.

History

Deposition	Aug 11, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 7, 2012	Provider: repository / Type: Initial release
Revision 1.1	Apr 4, 2012	Group: Database references
Revision 1.2	Jan 24, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3	Jun 13, 2018	Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code
Revision 1.4	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5	Feb 28, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3tdo.cif.gz	498.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3tdo.ent.gz	417.4 KB	Display	PDB format
PDBx/mmJSON format	3tdo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3tdo_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	3tdo_full_validation.pdf.gz	1.3 MB	Display
Data in XML	3tdo_validation.xml.gz	50.2 KB	Display
Data in CIF	3tdo_validation.cif.gz	67.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/td/3tdo ftp://data.pdbj.org/pub/pdb/validation_reports/td/3tdo	HTTPS FTP

-
Related structure data

Related structure data	3tdpC 3tdrC 3tdsC 3tdxC 3te0C 3te1C 3te2C 3tex C: citing same article (ref.)
Similar structure data	3tds-d 3tdx-d 3te1-d 3te2-d 4fc4-1 3tdr-1 3te0-d 3tdr-2 3kcu-d 3tdp-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#173 - May 2014 Aquaporin similarity (1)

Deposited unit

A: Putative formate/nitrite transporter

B: Putative formate/nitrite transporter

C: Putative formate/nitrite transporter

D: Putative formate/nitrite transporter

E: Putative formate/nitrite transporter

hetero molecules

144 kDa, 5 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)	98.824, 118.739, 149.822
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein

Putative formate/nitrite transporter

Mass: 28267.441 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Peptoclostridium difficile (strain 630) (bacteria)
Strain: 630 / Gene: CD630_22300 / Plasmid: pBad / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q186B7

#2: Chemical

ChemComp-PG4 / TETRAETHYLENE GLYCOL

Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM

#3: Sugar

ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside

Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C₁₄H₂₈O₆ / Comment: detergent*YM

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 198 / 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: 3.11 Å³/Da / Density % sol: 60.44 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: PEG 400, pH 7.5, vapor diffusion, temperature 298K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X25 / Wavelength: 0.975 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.975 Å / Relative weight: 1

Reflection

Resolution: 2.197→50 Å / Num. obs: 90263 / % possible obs: 99.9 % / Redundancy: 9.7 % / R_merge(I) obs: 0.078 / Net I/σ(I): 8.4

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
2.197-2.24	9.5	0.898	1	100
2.24-2.28	9.5	0.751	1	100
2.28-2.32	9.6	0.675	1	100
2.32-2.37	9.6	0.589	1	100
2.37-2.42	9.6	0.486	1	100
2.42-2.48	9.6	0.425	1	100
2.48-2.54	9.6	0.375	1	100
2.54-2.61	9.6	0.326	1	100
2.61-2.69	9.7	0.279	1	100
2.69-2.77	9.7	0.228	1	100
2.77-2.87	9.7	0.191	1	100
2.87-2.99	9.7	0.157	1	100
2.99-3.12	9.7	0.129	1	100
3.12-3.29	9.7	0.105	1	100
3.29-3.49	9.8	0.09	1	100
3.49-3.76	9.8	0.08	1	100
3.76-4.14	9.8	0.064	1	100
4.14-4.74	9.8	0.052	1	100
4.74-5.97	9.8	0.047	1	100
5.97-50	9.3	0.043	1	99

-
Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.7.1_743	refinement
PDB_EXTRACT	3.1	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.197→49.412 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.42 / σ(F): 1.34 / Phase error: 20.24 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2172	1999	2.22 %
R_work	0.1798	-	-
obs	0.1807	90161	99.85 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 63.375 Å² / k_sol: 0.33 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-6.4307 Å²	0 Å²	0 Å²
2-	-	2.1892 Å²	-0 Å²
3-	-	-	13.2051 Å²

Refinement step

Cycle: LAST / Resolution: 2.197→49.412 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9569	0	165	198	9932

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	9890
X-RAY DIFFRACTION	f_angle_d	1.124	13366
X-RAY DIFFRACTION	f_dihedral_angle_d	15.152	3424
X-RAY DIFFRACTION	f_chiral_restr	0.082	1686
X-RAY DIFFRACTION	f_plane_restr	0.005	1583

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 (%)
2.1973-2.2523	0.2624	139	0.2295	6137	X-RAY DIFFRACTION	99
2.2523-2.3132	0.2657	142	0.2199	6214	X-RAY DIFFRACTION	100
2.3132-2.3812	0.2519	140	0.2082	6246	X-RAY DIFFRACTION	100
2.3812-2.4581	0.2286	142	0.1917	6262	X-RAY DIFFRACTION	100
2.4581-2.5459	0.2681	141	0.1771	6233	X-RAY DIFFRACTION	100
2.5459-2.6479	0.2241	142	0.1846	6267	X-RAY DIFFRACTION	100
2.6479-2.7684	0.2251	143	0.1743	6262	X-RAY DIFFRACTION	100
2.7684-2.9143	0.2118	142	0.1815	6283	X-RAY DIFFRACTION	100
2.9143-3.0969	0.2146	142	0.1732	6283	X-RAY DIFFRACTION	100
3.0969-3.3359	0.229	143	0.1845	6277	X-RAY DIFFRACTION	100
3.3359-3.6715	0.215	144	0.1779	6351	X-RAY DIFFRACTION	100
3.6715-4.2026	0.1915	144	0.1666	6343	X-RAY DIFFRACTION	100
4.2026-5.2938	0.2097	146	0.1633	6405	X-RAY DIFFRACTION	100
5.2938-49.4245	0.2158	149	0.1904	6599	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	0.8635	-0.2001	-0.6163	3.7407	1.3905	2.3133	-0.2468	0.2987	-0.3144	-0.6396	0.2442	-0.6493	0.4485	0.1529	0.0548	0.8797	-0.1647	0.4007	0.5713	-0.1088	0.4208	26.6738	25.0631	-10.293
2	1.6349	0.6612	0.4284	5.5831	1.1384	2.6058	-0.1687	0.1493	-0.1269	-0.4467	0.106	0.2333	-0.0714	0.0305	0.0764	0.268	-0.0447	-0.0369	0.3014	-0.0031	0.2562	9.2239	18.7323	6.8163
3	1.3286	-0.1463	-0.6888	1.4554	0.0768	0.6426	-0.0954	0.5514	-0.293	-0.9477	0.1381	-0.0245	-0.0707	-0.0953	0.1444	0.7105	-0.1126	0.0014	0.485	-0.1354	0.3275	13.4058	17.7664	-8.9968
4	4.1881	-2.5174	2.5038	2.892	-0.5141	2.8668	-0.3756	-0.1337	-0.2239	-0.5984	0.6828	1.3307	0.1568	-1.2351	-0.3694	0.3408	-0.0662	-0.1455	0.4681	-0.0687	0.7505	-6.4302	16.3547	6.8766
5	1.033	-0.1662	0.3308	3.0232	0.7448	0.883	-0.1614	0.2543	-0.0583	-0.7751	0.0858	0.3657	-0.1198	-0.0079	0.0439	0.4207	-0.0573	-0.1001	0.3978	-0.0277	0.2421	6.3753	24.3711	-0.5944
6	3.6948	-0.9678	1.5067	4.791	0.5641	3.0715	0.0384	0.8758	0.0248	-0.9624	0.1609	-0.6042	-0.1087	0.6047	-0.1906	0.9044	-0.2369	0.171	0.6002	-0.0207	0.2019	20.198	36.9593	-12.7466
7	4.1731	1.0016	2.4927	4.3886	2.8874	6.6418	-0.0752	0.6504	-0.2715	-0.7007	0.5271	-0.6864	-0.036	0.9829	-0.3064	0.4466	-0.0993	0.1927	0.3978	-0.0317	0.5343	32.2207	51.9112	1.3782
8	3.0541	0.9432	-0.559	3.4901	-0.8324	3.9673	-0.1046	0.3595	0.2321	-0.4505	0.1402	0.433	-0.1615	-0.4725	-0.0471	0.2672	-0.0162	-0.0268	0.2536	-0.0123	0.2461	9.7532	41.4611	6.1804
9	3.0194	-2.0218	0.4409	1.4054	0.1456	3.8721	-0.0733	0.3493	0.3987	-0.5762	0.1589	-0.4109	-0.3662	-0.0564	-0.1562	0.4775	-0.0672	0.1053	0.4201	0.0193	0.4669	26.5437	57.7994	2.6942
10	6.8463	2.1924	0.4054	3.9655	1.1211	1.7347	-0.1378	1.0167	0.6258	-0.9237	0.4499	0.1029	-0.2103	-0.2025	-0.2018	0.6228	0.0468	-0.0887	0.3931	0.1237	0.3347	12.086	50.778	-4.7392
11	1.7113	0.5045	-1.4336	0.1796	-0.6125	2.4495	0.0173	0.0594	0.5603	-0.3046	0.0664	1.3608	-0.2752	-0.432	0.1389	0.2606	0.0603	-0.2095	0.4646	0.0105	0.7973	-5.1728	46.5018	7.2687
12	2.0561	1.0301	1.052	3.979	-0.0225	1.6884	-0.0777	0.1097	0.3039	-0.3219	0.033	0.1433	-0.1226	-0.0001	0.0626	0.3202	-0.0101	0.0361	0.2824	-0.0127	0.3019	14.0236	48.7315	10.8819
13	0.9234	0.3529	-1.0457	3.9732	0.2983	1.9175	0.0955	-0.2664	0.1349	-0.5046	0.0155	0.766	-0.2448	-0.8626	0.06	0.4465	0.0656	-0.1443	0.3998	0.1243	0.6208	3.0858	56.1818	3.3656
14	4.0138	-2.0691	-0.5456	6.623	-1.992	7.4937	0.2498	0.3811	0.8382	-0.1625	0.1145	-0.8046	-0.3763	0.8209	-0.2857	0.4033	-0.0782	0.1242	0.3485	-0.0899	0.5751	31.0818	60.4194	12.5753
15	3.8767	-3.8173	3.4236	7.9539	-5.629	5.1981	-0.3865	0.0882	0.1292	0.3226	-0.1559	-1.7301	-0.2769	0.6074	0.3456	0.3994	0.078	0.0659	0.3995	-0.1444	1.0133	34.0366	4.7473	9.8604
16	1.2136	-1.2819	0.5058	5.3313	0.6234	3.1285	-0.2026	-0.8982	-0.6502	0.8113	0.1544	0.0068	0.4568	0.0728	0.1547	0.429	-0.0231	-0.0005	0.3097	0.1143	0.4219	18.3528	9.2957	29.8806
17	5.874	-0.7794	-1.4733	5.9672	0.8178	5.2867	-0.2973	-0.2131	-0.348	0.3891	-0.059	0.7563	0.1334	-0.6749	0.1253	0.3405	-0.0559	0.0874	0.4653	0.0106	0.3689	6.1908	18.9769	24.5801
18	3.2311	-1.8996	-0.7752	5.3833	1.5463	3.226	0.256	0.3282	-0.3675	-0.2126	-0.1257	-1.2784	0.4072	0.438	-0.1078	0.381	-0.0107	-0.0903	0.3193	0.0361	0.6231	25.9354	11.8268	22.8353
19	2.7138	-1.6111	2.094	4.2843	-2.6158	3.5936	-0.2944	0.2418	-1.1553	-0.2756	0.0486	-0.8348	0.4296	0.4424	0.2217	0.3234	-0.0096	0.0669	0.3154	-0.0824	0.8494	27.3979	-0.2291	9.6495
20	3.6344	0.3992	-1.6811	2.3478	0.4195	6.9797	-0.0713	-0.4477	-1.0618	0.5036	-0.1272	-0.4236	-0.3144	0.5559	0.1154	0.569	-0.0028	-0.0435	0.3415	0.1451	0.7439	23.0215	-1.1831	26.7856
21	3.8113	-0.7503	-0.1473	0.9822	-0.086	2.4399	0.0244	-0.5219	-0.261	0.9792	-0.4974	0.7176	0.2966	-0.523	0.1039	0.7032	-0.1709	0.2701	0.4351	0.0551	0.5772	4.0703	6.2491	33.4385
22	1.6934	2.2801	0.7324	4.5478	0.9886	1.6338	-0.1085	0.0645	-0.6104	0.1534	0.2017	-0.7103	0.1597	0.2967	-0.0373	0.2534	0.007	0.0662	0.3029	0.0009	0.3874	16.9008	12.1231	14.1763
23	4.7866	0.7914	-0.2893	1.6807	0.6094	0.5736	0.0532	-0.7842	-0.7845	1.0927	-0.0588	-0.1171	0.5723	-0.2174	-0.032	0.7031	-0.0641	0.0638	0.4426	0.1302	0.5217	10.0234	2.2471	30.8517
24	6.3058	1.91	-1.779	4.8409	-2.721	2.955	0.2118	0.0149	-1.1167	0.536	-0.1577	0.0139	-0.6272	-0.2075	-0.0571	0.4152	0.0009	0.0856	0.2575	-0.0115	0.6386	12.0674	-3.3943	19.5093
25	1.2591	-1.2609	2.5172	1.8438	-1.8962	5.6986	-0.1224	0.7997	-0.0801	-1.0279	0.2976	-1.1666	0.5388	1.0547	0.1765	0.5024	-0.0392	0.2715	0.4825	-0.1139	0.6154	25.2244	4.392	-0.6332
26	3.0426	0.886	0.0371	3.7077	-0.1332	1.4208	0.0966	-0.2748	0.3369	0.3046	-0.0122	-0.3049	0.0012	0.1639	-0.0624	0.3108	0.0107	0.0066	0.3519	-0.1307	0.2712	25.2993	48.7981	27.6326
27	1.1148	0.6866	-0.3465	1.8091	0.122	1.1479	0.078	-0.1973	0.1519	0.4161	0.0173	-0.4848	-0.0915	0.3148	-0.0379	0.3042	-0.0327	-0.0668	0.3283	-0.1825	0.4365	30.0134	54.8884	29.979
28	1.5134	0.3776	0.619	3.9181	0.1503	1.5992	0.1199	-0.2033	0.3158	0.6024	-0.141	-0.1039	-0.072	-0.1016	-0.0152	0.3852	-0.0443	0.0091	0.4145	-0.1003	0.3291	18.5893	47.7869	33.703
29	1.9966	-0.6012	-1.4104	4.2684	0.7475	2.7925	0.7884	-0.3027	0.3128	0.6174	-0.3147	0.4524	-0.1793	-0.3445	-0.1232	0.562	-0.0957	0.1318	0.5842	-0.2403	0.4605	17.2466	58.2695	39.7429
30	4.5472	2.8353	3.5688	3.1718	0.262	7.1242	0.2848	0.1848	-0.615	0.3032	0.2447	-1.1083	0.6099	1.0447	-0.0255	0.6134	0.0628	-0.4397	0.5336	-0.1036	0.7868	41.9315	41.2768	40.8584
31	2.18	-0.119	0.482	2.5243	0.6485	0.9652	0.0668	-0.6984	-0.2238	1.0987	0.0615	-0.869	0.2454	0.2087	-0.1353	0.4351	-0.073	-0.2485	0.3162	0.0781	0.3234	28.7409	26.6651	37.9051
32	0.2261	0.3069	0.0353	1.0676	0.2914	1.0276	-0.0224	-0.753	-0.3774	1.179	0.0644	-0.8217	0.3443	0.6348	-0.2073	0.7318	0.0056	-0.7323	0.515	0.1475	0.1448	34.6907	24.7149	43.4662
33	3.3582	-0.3139	1.3171	2.4895	-1.9189	1.8298	0.1472	-1.1857	-0.0383	0.6523	0.3967	0.4395	0.1258	-0.6391	-0.4063	1.1139	-0.199	0.2223	0.8478	-0.0042	0.3375	11.4431	30.1117	50.3867
34	2.9697	-1.3066	-0.0767	1.8184	-1.0555	4.1205	0.0248	-0.5585	-0.2688	0.897	-0.0644	-0.6315	0.3438	0.3089	0.1813	0.5261	-0.039	-0.1435	0.3243	0.0334	0.3239	25.0149	19.1975	33.878
35	2.7205	-0.3122	0.7997	9.809	3.8822	3.6818	-0.4726	-0.7634	0.148	0.8869	0.1846	0.8929	0.1555	0.165	0.2402	1.2322	-0.0418	-0.1204	0.7299	0.0141	0.3864	18.873	28.5633	51.2119
36	1.9294	0.743	1.0932	2.5412	-1.2666	2.3156	0.234	-0.6131	0.0308	1.0119	-0.4321	-0.167	-0.198	0.0638	0.1063	1.1607	-0.1251	-0.4038	0.7265	0.1591	0.365	24.8825	18.0037	51.3684
37	2.4415	-0.2049	1.8398	2.6146	0.7558	3.8878	-0.0702	-0.1791	-0.1836	0.522	0.142	-0.9831	0.4242	0.5807	0.2225	0.6999	0.0741	-0.3386	0.4405	0.1274	0.8579	35.4076	7.7009	34.4964
38	3.3528	-1.2993	2.6402	1.3377	-0.6192	2.9907	0.1577	-0.1392	0.4209	-0.0928	-0.468	-0.395	-0.0227	0.44	0.3644	0.5123	0.1052	-0.3711	1.0937	0.2107	1.2388	45.6259	-0.9448	30.4968

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 0:23)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 24:82)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 83:129)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 130:152)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 153:242)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 243:256)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 0:23)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 24:82)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 83:100)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 101:129)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 130:152)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 153:214)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 215:242)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 243:256)
15	X-RAY DIFFRACTION	15	chain 'D' and (resseq 0:23)
16	X-RAY DIFFRACTION	16	chain 'D' and (resseq 24:55)
17	X-RAY DIFFRACTION	17	chain 'D' and (resseq 56:69)
18	X-RAY DIFFRACTION	18	chain 'D' and (resseq 70:82)
19	X-RAY DIFFRACTION	19	chain 'D' and (resseq 83:100)
20	X-RAY DIFFRACTION	20	chain 'D' and (resseq 101:129)
21	X-RAY DIFFRACTION	21	chain 'D' and (resseq 130:152)
22	X-RAY DIFFRACTION	22	chain 'D' and (resseq 153:197)
23	X-RAY DIFFRACTION	23	chain 'D' and (resseq 198:221)
24	X-RAY DIFFRACTION	24	chain 'D' and (resseq 222:243)
25	X-RAY DIFFRACTION	25	chain 'D' and (resseq 244:256)
26	X-RAY DIFFRACTION	26	chain 'E' and (resseq 0:68)
27	X-RAY DIFFRACTION	27	chain 'E' and (resseq 69:129)
28	X-RAY DIFFRACTION	28	chain 'E' and (resseq 130:214)
29	X-RAY DIFFRACTION	29	chain 'E' and (resseq 215:242)
30	X-RAY DIFFRACTION	30	chain 'E' and (resseq 243:256)
31	X-RAY DIFFRACTION	31	chain 'C' and (resseq 0:69)
32	X-RAY DIFFRACTION	32	chain 'C' and (resseq 70:129)
33	X-RAY DIFFRACTION	33	chain 'C' and (resseq 130:152)
34	X-RAY DIFFRACTION	34	chain 'C' and (resseq 153:197)
35	X-RAY DIFFRACTION	35	chain 'C' and (resseq 198:221)
36	X-RAY DIFFRACTION	36	chain 'C' and (resseq 222:242)
37	X-RAY DIFFRACTION	37	chain 'C' and (resseq 243:253)
38	X-RAY DIFFRACTION	38	chain 'C' and (resseq 254:265)

-
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