PDB-6xub: Structure of coproheme decarboxylase from Corynebacterium diphter...

ID or keywords:

Entry

Database: PDB / ID: 6xub

Title

Structure of coproheme decarboxylase from Corynebacterium diphteriae in complex with monovinyl monopropionyl deuteroheme

Components

Chlorite dismutase

Keywords

OXIDOREDUCTASE / Coproheme decarboxylase / heme b biosynthesis / decarboxylation / ferredoxin like / actinobacterial

Function / homology

Function and homology information

oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor / hydrogen peroxide-dependent heme synthase / heme B biosynthetic process / oxidoreductase activity / heme binding / metal ion binding
Similarity search - Function

Biological species

Corynebacterium diphtheriae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.78 Å

Authors

Michlits, H. / Lier, B. / Pfanzagl, V. / Djinovic-Carugo, K. / Furtmueller, P.G. / Oostenbrink, C. / Obinger, C. / Hofbauer, S.

Funding support

Austria, 1items

Citation

Journal: Acs Catalysis / Year: 2020
Title: Actinobacterial Coproheme Decarboxylases Use Histidine as a Distal Base to Promote Compound I Formation.
Authors: Michlits, H. / Lier, B. / Pfanzagl, V. / Djinovic-Carugo, K. / Furtmuller, P.G. / Oostenbrink, C. / Obinger, C. / Hofbauer, S.

History

Deposition	Jan 17, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 22, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jun 10, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jan 24, 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	6xub.cif.gz	689.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6xub.ent.gz	584.5 KB	Display	PDB format
PDBx/mmJSON format	6xub.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	6xucC 3dtzS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6xuc-d 3dtz-d 6fxj-d 5loq-d 6fxq-d 6oe8-d 6vsa-d 4wws-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

Deposited unit

A: Chlorite dismutase

B: Chlorite dismutase

C: Chlorite dismutase

D: Chlorite dismutase

E: Chlorite dismutase

hetero molecules

140 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: light scattering

Unit cell

Length a, b, c (Å)	60.969, 123.382, 78.009
Angle α, β, γ (deg.)	90.000, 98.710, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Chlorite dismutase Mass: 27288.961 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: B11Q_01470, BT093_04375 / Production host: Escherichia coli (E. coli) / Variant (production host): Tuner / References: UniProt: A0A2T1BSE4, UniProt: Q6NGV6*PLUS
#2: Chemical	ChemComp-VOV / harderoheme (III) Mass: 662.513 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C₃₅H₃₄FeN₄O₆ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 737 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 43.98 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: PEG 33500, MgCl2

-
Data collection

Diffraction	Mean temperature: 170 K / Ambient temp details: cryo stream / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 4, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 1.5645→48.1924 Å / Num. obs: 156754 / % possible obs: 98.02 % / Redundancy: 3.05 % / CC_1/2: 0.996 / Net I/σ(I): 6.33
Reflection shell	Resolution: 1.5645→1.621 Å / Num. unique obs: 14679 / CC_1/2: 0.223 / % possible all: 92.16

-
Processing

Software

Name	Version	Classification
PHENIX	1.15.2_3472	refinement
PDB_EXTRACT	3.25	data extraction
EDNA		data reduction
EDNA		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3DTZ

3dtz

Resolution: 1.78→48.1891 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.39

	R_factor	Num. reflection	% reflection
R_free	0.2272	5271	4.95 %
R_work	0.1737	-	-
obs	0.1764	106562	97.88 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 376.04 Å² / B_iso mean: 44.0519 Å² / B_iso min: 18.6 Å²

Refinement step

Cycle: final / Resolution: 1.78→48.1891 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9310	0	385	737	10432
B_iso mean	-	-	58.85	38.88	-
Num. residues	-	-	-	-	1142

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.78-1.8002	0.4103	167	0.3728	2951	86
1.8002-1.8214	0.3797	157	0.3554	3268	95
1.8214-1.8436	0.35	158	0.3428	3372	97
1.8436-1.867	0.3317	157	0.3255	3368	97
1.867-1.8915	0.3108	185	0.3032	3388	99
1.8915-1.9174	0.3109	153	0.2926	3433	99
1.9174-1.9448	0.3104	206	0.2647	3364	99
1.9448-1.9739	0.2857	166	0.24	3435	99
1.9739-2.0047	0.2966	164	0.2378	3423	99
2.0047-2.0376	0.27	185	0.2258	3411	99
2.0376-2.0727	0.2724	196	0.2156	3372	99
2.0727-2.1104	0.2746	175	0.2001	3439	100
2.1104-2.151	0.252	151	0.1926	3441	100
2.151-2.1949	0.2796	159	0.1902	3451	100
2.1949-2.2426	0.2512	192	0.1894	3416	99
2.2426-2.2948	0.2106	206	0.1852	3375	99
2.2948-2.3522	0.2674	175	0.1802	3391	98
2.3522-2.4158	0.2626	179	0.1709	3355	98
2.4158-2.4869	0.23	174	0.1704	3423	99
2.4869-2.5671	0.248	196	0.1751	3384	99
2.5671-2.6589	0.212	151	0.1693	3469	99
2.6589-2.7653	0.2314	172	0.1695	3408	99
2.7653-2.8912	0.2497	166	0.1737	3404	99
2.8912-3.0436	0.2429	176	0.1809	3402	98
3.0436-3.2342	0.2543	189	0.1746	3313	97
3.2342-3.4839	0.219	189	0.159	3297	96
3.4839-3.8343	0.2028	166	0.1438	3399	97
3.8343-4.3888	0.1723	207	0.1192	3361	98
4.3888-5.5282	0.1592	172	0.1212	3377	97
5.5282-48.1891	0.1947	182	0.1643	3401	97

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	0.5053	0.1204	-0.1168	0.9842	-0.0556	0.1064	-0.1479	-0.0989	0.0619	0.1048	0.0651	0.1776	-0.0367	-0.2559	0.0015	0.2724	0.0223	0.0339	0.316	0.0113	0.2367	31.9865	79.6666	81.8599
2	0.7736	-0.464	0.184	1.2028	0.5055	0.326	-0.0933	-0.2002	-0.1058	0.204	-0.0182	0.355	-0.0939	-0.2228	-0.0145	0.2717	0.0153	0.077	0.3702	0.0059	0.3328	25.2364	80.1016	81.7713
3	0.0388	-0.0321	-0.0413	0.0241	0.0674	0.1957	-0.0333	0.2225	-0.3442	0.1633	0.0362	0.4351	0.3146	-0.13	0.0004	0.2668	-0.0175	0.0755	0.3101	0.0381	0.3696	27.8485	69.5107	80.3547
4	0.1552	-0.3425	0.0188	0.7719	0.0182	-0.0113	-0.0734	-0.1969	0.0143	-0.0028	0.0501	0.1144	-0.0564	-0.1489	0	0.3058	0.0016	0.0108	0.3489	0.0185	0.2884	38.0202	79.5798	80.3276
5	0.0364	0.0473	-0.0489	0.1041	-0.0071	0.1179	0.0155	-0.2446	0.2248	0.4108	0.0921	-0.0579	-0.2442	-0.0092	0.0005	0.3029	0.0563	0.0264	0.3757	-0.0093	0.2288	36.9495	88.2926	90.2822
6	0.0962	0.0782	0.0016	0.3989	0.0535	-0.0226	-0.0968	-0.0437	-0.2142	0.0072	0.069	-0.0967	0.0469	-0.0149	-0.0029	0.2169	0.0238	-0.0121	0.2941	-0.0007	0.2569	49.7759	86.3939	74.9889
7	0.2304	0.2822	-0.1056	0.334	-0.1408	0.0744	0.1835	-0.3462	0.4126	0.1084	-0.0175	-0.3805	-0.1127	-0.0669	0.0026	0.2758	0.0268	-0.0418	0.3067	-0.0307	0.3075	55.3797	94.9845	83.0706
8	-0.0107	0.0842	0.0067	0.3474	0.0339	-0.0047	0.0037	-0.1114	-0.0535	0.1996	-0.0868	0.1351	-0.0074	-0.1226	0.0002	0.2576	0.032	0.0012	0.304	-0.016	0.2379	41.6627	86.709	80.3381
9	0.0696	0.0145	-0.026	0.0843	0.1159	0.1556	0.1212	-0.118	0.1192	0.0218	0.1095	-0.0131	-0.2294	-0.0328	-0.0006	0.3183	0.0222	-0.0079	0.3438	-0.0133	0.345	41.2587	100.2138	76.5328
10	0.3392	-0.0828	0.2387	0.0755	-0.0262	0.0758	0.0016	-0.1709	-0.0707	0.0209	-0.0206	0.057	-0.0877	-0.0067	0	0.2404	0.0069	0.0186	0.2947	-0.0021	0.307	34.312	89.559	74.4471
11	0.6437	0.1778	-0.0853	0.782	0.1252	1.1429	-0.0807	-0.1038	-0.266	-0.0008	-0.0042	0.1509	0.1886	-0.1014	0.0001	0.2737	-0.0109	0.0194	0.2581	0.0278	0.3569	37.929	54.2448	65.9681
12	0.2836	-0.1694	-0.0434	0.6037	0.1378	0.2108	-0.0097	-0.0576	-0.1086	0.0995	0.0187	-0.0771	0.0268	0.0614	-0	0.2613	0.0124	0.0079	0.2921	0.0315	0.3124	51.1369	61.648	66.6574
13	0.0629	0.0735	-0.0719	0.1246	-0.026	0.0751	0.0753	0.0823	0.1552	0.0416	-0.0726	-0.5735	-0.089	-0.1632	0.0057	0.3377	0.024	0.042	0.342	0.0093	0.4827	68.0134	68.6858	71.1266
14	0.0777	0.0873	-0.058	0.0739	-0.064	0.0444	0.182	-0.0165	-0.059	0.1677	0.1119	-0.1453	0.1432	0.0258	0.0057	0.2947	0.0228	-0.0392	0.2755	0.0358	0.3374	55.6264	61.9835	77.6746
15	0.1348	0.1715	0.1351	0.5803	0.1898	0.1242	-0.0134	0.047	-0.1968	-0.0185	0.0037	-0.047	-0.2535	-0.1376	-0.0004	0.2701	0.0134	0.0035	0.2814	0.0123	0.3263	50.4329	63.9477	66.6984
16	0.0815	-0.0228	0.076	0.0671	-0.0272	0.0515	-0.2961	-0.1675	-0.5182	0.222	0.0304	-0.2032	0.0467	0.1197	-0.0005	0.287	0.0297	0.0107	0.2911	0.009	0.3178	51.9289	71.4182	80.5034
17	0.4117	-0.1589	0.0237	0.1336	0.2361	0.5045	-0.0475	-0.034	-0.216	0.1117	0.0425	-0.1406	0.0619	-0.0219	0	0.2276	0.0142	0.0166	0.2603	0.0379	0.2803	43.0098	66.8207	72.1723
18	0.5353	-0.1099	-0.0333	0.4058	-0.6108	0.9633	-0.0643	0.0372	0.0749	-0.0424	0.0781	0.1867	-0.1721	-0.1359	0.0004	0.2948	0.0262	-0.0293	0.3172	0.005	0.3888	24.8109	101.5262	61.8492
19	0.316	0.0804	-0.0501	0.2117	-0.007	0.6708	0.035	0.0211	0.2639	-0.2748	-0.0825	0.4479	-0.1102	-0.378	0.034	0.2865	0.0673	-0.1042	0.3778	-0.0477	0.5616	14.4461	102.4482	60.2828
20	0.5604	0.0929	0.0696	0.7804	-0.1174	0.5213	-0.0319	0.0129	0.0872	-0.1368	-0.0125	0.1464	-0.1162	-0.0705	0	0.299	0.0358	-0.0192	0.2636	-0.0229	0.2993	30.9112	100.9233	62.1892
21	0.2746	0.1197	-0.0854	0.0541	-0.0488	0.0253	0.1607	-0.0375	0.1486	-0.4273	0.0707	-0.1053	0.015	0.4092	0.0316	0.3953	-0.0507	-0.0037	0.2734	-0.0274	0.3015	52.5686	111.7195	60.5327
22	0.5473	-0.0491	0.128	0.2043	0.2449	0.3204	-0.0181	-0.0248	0.1122	-0.2637	-0.0181	0.1314	-0.1456	0.0451	0.0001	0.346	0.0001	-0.025	0.2386	-0.0138	0.2707	37.3613	106.0429	57.8048
23	0.0695	0.0418	-0.1915	0.0588	-0.1155	0.3845	-0.0003	0.0639	0.116	-0.1359	-0.0469	0.0474	-0.185	-0.0975	-0	0.3547	-0.0009	-0.0075	0.283	0.0114	0.2849	45.2293	102.8239	51.1068
24	1.264	-0.2273	-0.0555	0.0438	0.1434	1.5766	0.0646	-0.0415	0.2589	-0.5593	-0.0533	0.3389	-0.0764	0.1261	0.4985	0.3701	0.0643	-0.1943	0.2202	0.0163	0.3949	20.1289	99.0917	49.3267
25	0.2744	-0.1653	-0.137	0.2369	0.3264	0.5151	-0.1062	0.1533	0.1219	-0.4741	0.0597	0.1943	0.0743	-0.1399	-0.0012	0.4699	0.005	-0.0232	0.2823	0.0499	0.3476	35.2618	97.1036	33.8335
26	0.8669	0.2104	0.2815	1.1684	-0.1653	0.506	-0.031	0.0825	0.1726	-0.0547	0.0262	0.271	0.0305	0.0175	0	0.3916	-0.0201	0.0099	0.2676	0.0138	0.2908	33.0697	90.4644	34.6786
27	0.0975	0.0394	-0.0927	0.0367	-0.0098	0.1123	-0.1347	0.2877	-0.0881	-0.0788	0.0437	-0.3478	-0.0986	0.1619	0.0001	0.4816	-0.1007	0.0595	0.3526	0.049	0.357	60.2194	98.0823	36.2233
28	0.0525	-0.0822	0.0818	0.137	-0.0273	0.2269	-0.0151	0.1433	0.2193	0.0364	0.1472	-0.0744	0.2034	0.1308	0.0015	0.4467	-0.023	0.055	0.3957	0.0301	0.2617	49.2768	90.6396	27.9908
29	0.6432	-0.3233	0.4623	0.1629	-0.2373	0.3071	0.0169	0.0441	0.1715	-0.1659	0.1031	-0.132	-0.1878	0.0227	-0.0001	0.4023	-0.0232	0.047	0.2692	0.0106	0.2757	42.6619	91.6821	38.0513
30	0.0165	0.0146	-0.0591	0.0078	-0.0478	0.1559	0.1063	0.1161	-0.1632	-0.3232	-0.1498	-0.243	0.0895	0.0014	0.0005	0.4455	-0.0264	0.0671	0.3723	-0.0044	0.2366	52.563	81.2004	31.5714
31	0.3425	-0.363	0.002	0.3549	-0.1501	0.4354	-0.1443	0.1746	0.0621	-0.3123	0.049	0.0425	-0.0458	0.0313	-0.0006	0.4011	-0.0329	-0.0166	0.2921	-0.0016	0.2423	40.4793	82.5747	35.8371
32	0.4458	-0.089	0.6327	0.3197	0.0443	0.8598	0.0834	0.1099	-0.2937	-0.0964	0.0552	0.2206	-0.04	-0.3502	0.0335	0.4084	-0.0283	0.0212	0.3507	-0.0155	0.3214	35.2971	62.5783	41.3086
33	0.4733	-0.144	0.2796	0.1454	-0.2312	0.2699	-0.0027	0.1114	-0.287	-0.2253	0.059	-0.0649	0.2158	0.0031	0.0029	0.4817	-0.0431	0.003	0.2935	-0.0828	0.3076	36.8368	58.6701	37.7516
34	0.1379	-0.0485	0.1055	0.153	0.0407	0.0952	-0.0883	0.0547	0.186	-0.6022	0.1139	0.2697	0.1916	0.0361	0.0001	0.4648	-0.0411	-0.0254	0.3159	-0.0407	0.3203	32.8185	67.3461	32.1322
35	0.4603	-0.2145	0.218	0.7521	-0.2266	0.0849	0.0186	0.1499	-0.1144	-0.0702	0.0217	-0.2692	0.1365	0.1652	-0	0.4483	0.036	0.0365	0.3814	-0.0682	0.3829	48.2395	64.411	36.7415
36	0.3962	0.0345	0.1855	0.0254	0.0847	0.3141	-0.0061	0.127	-0.1243	-0.3672	0.0089	-0.1241	0.1133	0.221	-0.0024	0.357	-0.0033	0.1107	0.3487	-0.0089	0.3388	62.2845	72.6823	44.0961
37	0.3326	0.3817	0.2003	0.4902	0.3955	0.4572	0.0021	0.2192	-0.0675	-0.2851	-0.0342	-0.1415	0.0356	0.121	-0.0001	0.3531	0.0346	0.0796	0.2955	-0.029	0.3017	54.5027	64.6023	42.2253
38	0.0615	-0.0474	-0.0922	0.0335	0.0713	0.1282	0.0781	-0.1124	0.0675	-0.0029	-0.1648	-0.061	0.2028	0.0987	0	0.3339	0.0194	0.048	0.3332	-0.0225	0.3653	58.2757	59.7527	52.7007
39	0.0196	0.035	-0.0106	0.0395	-0.0791	0.1147	-0.184	0.0259	-0.179	0.0099	0.1843	-0.1318	-0.2489	0.0711	0.0001	0.2985	-0.022	0.0637	0.3144	-0.006	0.29	58.9398	73.4729	51.1087
40	0.1871	-0.1113	-0.0452	0.0975	-0.1184	0.3072	0.3326	-0.0973	-0.5173	-0.0358	-0.1495	-0.1581	0.2203	-0.1779	0	0.3991	-0.0255	-0.0417	0.2744	-0.0199	0.4125	37.2025	54.2954	46.4567

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 33 )	A	6 - 33
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 34 through 78 )	A	34 - 78
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 79 through 92 )	A	79 - 92
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 93 through 118 )	A	93 - 118
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 119 through 130 )	A	119 - 130
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 131 through 147 )	A	131 - 147
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 148 through 165 )	A	148 - 165
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 166 through 191 )	A	166 - 191
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 192 through 203 )	A	192 - 203
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 204 through 235 )	A	204 - 235
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 6 through 92 )	B	6 - 92
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 93 through 147 )	B	93 - 147
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 148 through 162 )	B	148 - 162
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 163 through 174 )	B	163 - 174
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 175 through 191 )	B	175 - 191
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 192 through 203 )	B	192 - 203
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 204 through 235 )	B	204 - 235
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 6 through 33 )	C	6 - 33
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 34 through 60 )	C	34 - 60
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 61 through 147 )	C	61 - 147
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 148 through 162 )	C	148 - 162
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 163 through 191 )	C	163 - 191
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 192 through 216 )	C	192 - 216
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 217 through 235 )	C	217 - 235
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 8 through 24 )	D	8 - 24
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 25 through 147 )	D	25 - 147
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 148 through 162 )	D	148 - 162
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 163 through 174 )	D	163 - 174
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 175 through 191 )	D	175 - 191
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 192 through 203 )	D	192 - 203
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 204 through 235 )	D	204 - 235
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 13 through 33 )	E	13 - 33
33	X-RAY DIFFRACTION	33	chain 'E' and (resid 34 through 78 )	E	34 - 78
34	X-RAY DIFFRACTION	34	chain 'E' and (resid 79 through 92 )	E	79 - 92
35	X-RAY DIFFRACTION	35	chain 'E' and (resid 93 through 130 )	E	93 - 130
36	X-RAY DIFFRACTION	36	chain 'E' and (resid 131 through 162 )	E	131 - 162
37	X-RAY DIFFRACTION	37	chain 'E' and (resid 163 through 191 )	E	163 - 191
38	X-RAY DIFFRACTION	38	chain 'E' and (resid 192 through 203 )	E	192 - 203
39	X-RAY DIFFRACTION	39	chain 'E' and (resid 204 through 216 )	E	204 - 216
40	X-RAY DIFFRACTION	40	chain 'E' and (resid 217 through 235 )	E	217 - 235

-
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