PDB-6tv9: Heme d1 biosynthesis associated Protein NirF in complex with dihy...

ID or keywords:

Entry

Database: PDB / ID: 6tv9

Title

Heme d1 biosynthesis associated Protein NirF in complex with dihydro-heme d1

Components

Protein NirF,Protein NirF

Keywords

UNKNOWN FUNCTION / 8-bladed beta-propeller / heme d1 biosynthesis / homodimer / ligand complex

Function / homology

Cytochrome cd1-nitrite reductase, C-terminal domain superfamily / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / cytoplasm / HEME D / Protein NirF

Function and homology information

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.893 Å

Authors

Kluenemann, T. / Layer, G. / Blankenfeldt, W.

Funding support

Germany, 1items

Citation

Journal: Febs J. / Year: 2021
Title: Crystal structure of NirF: insights into its role in heme d 1 biosynthesis.
Authors: Klunemann, T. / Nimtz, M. / Jansch, L. / Layer, G. / Blankenfeldt, W.

History

Deposition	Jan 9, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 22, 2020	Provider: repository / Type: Initial release
Revision 1.1	Sep 30, 2020	Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Jan 13, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3	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 / pdbx_validate_chiral Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6tv9.cif.gz	1.6 MB	Display	PDBx/mmCIF format
PDB format	pdb6tv9.ent.gz	1.4 MB	Display	PDB format
PDBx/mmJSON format	6tv9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6tv9_validation.pdf.gz	3.4 MB	Display	wwPDB validaton report
Full document	6tv9_full_validation.pdf.gz	3.4 MB	Display
Data in XML	6tv9_validation.xml.gz	119 KB	Display
Data in CIF	6tv9_validation.cif.gz	167.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tv/6tv9 ftp://data.pdbj.org/pub/pdb/validation_reports/tv/6tv9	HTTPS FTP

-
Related structure data

Related structure data	6tv2SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6tv2-2 6tv2-3 6tv2-1 6tv2-4 1r1j-d 5lv0-1 4bmk-d 2wge-1 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) 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

6tv2SC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Protein NirF,Protein NirF

B: Protein NirF,Protein NirF

C: Protein NirF,Protein NirF

D: Protein NirF,Protein NirF

E: Protein NirF,Protein NirF

F: Protein NirF,Protein NirF

G: Protein NirF,Protein NirF

H: Protein NirF,Protein NirF

hetero molecules

342 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein NirF,Protein NirF

hetero molecules

H: Protein NirF,Protein NirF

hetero molecules

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

2

B: Protein NirF,Protein NirF

E: Protein NirF,Protein NirF

hetero molecules

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

3

C: Protein NirF,Protein NirF

G: Protein NirF,Protein NirF

hetero molecules

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

4

D: Protein NirF,Protein NirF

hetero molecules

F: Protein NirF,Protein NirF

hetero molecules

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

Unit cell

Length a, b, c (Å)	101.197, 149.443, 110.174
Angle α, β, γ (deg.)	90.000, 98.480, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Protein NirF,Protein NirF Mass: 41999.281 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Gene: nirF, PA0516 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q51480
#2: Chemical	ChemComp-DHE / HEME D Mass: 712.484 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₁₀ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1533 / 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: 2.45 Å³/Da / Density % sol: 49.84 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 10% (w/v) PEG 4000 20% (v/v) glycerol 0.02M Morpheus amino acid Mix 0.1M MOPS/HEPES pH 7.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.7265 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 12, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.7265 Å / Relative weight: 1
Reflection	Resolution: 1.89→100.09 Å / Num. obs: 149789 / % possible obs: 93 % / Redundancy: 6.1 % / CC_1/2: 0.991 / R_pim(I) all: 0.076 / Net I/σ(I): 6.1
Reflection shell	Resolution: 1.89→2.14 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 7472 / CC_1/2: 0.742 / R_pim(I) all: 0.342 / % possible all: 52.6

-
Processing

Software

Name	Version	Classification
PHENIX	dev 3742	refinement
PDB_EXTRACT	3.25	data extraction
DIALS		data reduction
STARANISO		data scaling
PHENIX		phasing
Aimless		data scaling

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 6TV2

6tv2

Resolution: 1.893→100.09 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2576	7421	4.96 %
R_work	0.2153	142287	-
obs	0.2174	149708	58.34 %

Solvent computation

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

Displacement parameters

B_iso max: 95.38 Å² / B_iso mean: 25.0315 Å² / B_iso min: 1.29 Å²

Refinement step

Cycle: final / Resolution: 1.893→100.09 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23312	0	616	1533	25461
B_iso mean	-	-	22.5	25.32	-
Num. residues	-	-	-	-	2976

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 (%)
1.8935-1.915	0.3	4	0.3084	114	1
1.915-1.9375	0.22	5	0.2967	194	2
1.9375-1.9612	0.3381	28	0.3062	278	4
1.9612-1.986	0.1962	26	0.2964	406	5
1.986-2.0121	0.3021	22	0.2897	558	7
2.0121-2.0397	0.3159	36	0.2599	763	9
2.0397-2.0688	0.2992	44	0.2915	1061	13
2.0688-2.0997	0.2953	76	0.2767	1530	19
2.0997-2.1325	0.3271	98	0.2716	2023	25
2.1325-2.1675	0.3119	142	0.2621	2629	32
2.1675-2.2049	0.3171	172	0.2637	3294	41
2.2049-2.245	0.3097	187	0.2588	3841	47
2.245-2.2882	0.3009	208	0.2476	4228	52
2.2882-2.3349	0.3018	229	0.2565	4545	56
2.3349-2.3856	0.3366	265	0.258	4899	61
2.3856-2.4411	0.3262	289	0.253	5253	65
2.4411-2.5022	0.313	306	0.2515	5620	70
2.5022-2.5699	0.2657	325	0.2535	6127	75
2.5699-2.6455	0.3099	344	0.2562	6618	82
2.6455-2.7309	0.2738	371	0.2362	7196	88
2.7309-2.8285	0.2846	413	0.2369	7722	95
2.8285-2.9417	0.276	417	0.2315	8078	99
2.9417-3.0756	0.2848	448	0.236	8129	100
3.0756-3.2378	0.279	421	0.223	8125	100
3.2378-3.4407	0.2392	445	0.206	8122	100
3.4407-3.7063	0.2414	432	0.1936	8160	100
3.7063-4.0793	0.2165	389	0.1793	8195	100
4.0793-4.6696	0.1923	430	0.1481	8136	100
4.6696-5.8831	0.2121	426	0.1782	8186	100
5.8831-100.09	0.2576	423	0.2388	8257	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	0.4902	0.2617	0.0373	0.9193	0.2561	0.4981	0.0916	0.1019	0.356	-0.0278	-0.0178	0.1428	-0.1345	-0.0141	-0.0149	0.1389	-0.024	0.0514	0.0864	0.0086	0.3162	46.4837	-58.2548	-8.5478
2	2.192	-0.7953	-0.3805	0.4775	0.6802	2.8665	0.0111	-0.2133	0.0821	0.0897	-0.0298	0.0951	-0.0027	0.0518	0.0161	0.1138	-0.0559	-0.0155	0.1458	0.0111	0.1871	68.0772	-56.9332	-7.1261
3	1.4147	0.4892	0.0517	0.8067	0.1471	0.5677	-0.099	0.3906	-0.1322	-0.1873	0.0849	-0.0895	-0.0153	0.1037	0.0156	0.1221	0.0063	0.0468	0.1696	0.0169	0.1249	63.0537	-69.4284	-20.488
4	0.541	0.0435	0.0966	0.1416	0.0319	0.0226	-0.0568	0.4098	-0.4859	-0.1017	0.1065	-0.1556	0.1315	0.007	0.0847	0.1452	-0.081	0.1211	0.3415	-0.2257	0.6309	67.6211	-51.6565	-69.5845
5	0.3123	0.0395	-0.0245	0.1296	-0.0193	0.0986	0.0506	0.0459	-0.3387	0.0242	-0.0187	-0.0563	0.0933	-0.0281	0.0067	0.0995	-0.0688	-0.0215	0.0672	-0.0596	0.6916	51.892	-57.6114	-55.1328
6	0.7809	0.2704	-0.2224	0.3141	-0.142	0.1137	-0.1486	0.4312	-0.103	-0.1789	0.0884	-0.111	0.0077	0.069	-0.1274	0.0551	-0.1345	0.1295	0.4179	-0.118	0.2241	45.2016	-43.9886	-73.2088
7	0.3403	0.1166	-0.0561	0.4293	0.1821	0.8469	-0.0278	-0.0829	0.0053	0.0689	0.0386	-0.081	0.0787	0.1031	-0.035	0.0834	0.0062	0.0036	0.0052	-0.0682	-0.0171	16.5935	-34.0137	-35.2785
8	0.5703	-0.1964	0.2003	0.3815	-0.2413	0.4882	0.0001	0.0194	0.1752	0.0343	-0.0138	0.0057	-0.1087	0.0153	0.0429	0.0823	-0.0007	0.0357	-0.0654	0.0388	0.0404	13.7091	-18.7779	-50.4951
9	1.1337	-0.188	-0.3205	0.833	0.2839	1.3372	0.0126	0.1461	0.1332	-0.117	-0.0116	0.0743	-0.0827	-0.1291	-0.0045	0.0568	-0.0029	-0.0217	0.0246	-0.0036	0.0247	-0.8812	-22.7246	-53.4604
10	1.0514	-0.2481	0.2698	1.4944	-0.753	0.4491	-0.0595	0.1441	0.0226	-0.095	0.0611	0.0839	0.117	0.0156	-0.0157	0.0315	-0.0111	0.0284	0.056	-0.0371	0.0559	-11.4352	-33.0804	-43.619
11	0.202	-0.018	0.1398	0.1244	0.0586	0.5267	-0.0381	-0.1249	-0.0147	0.0999	0.0336	0.0605	0.0037	-0.044	0.001	0.1136	0.0317	0.078	0.074	-0.0109	-0.0353	-2.4547	-38.4217	-32.1041
12	0.1336	-0.0212	0.0015	0.0702	0.1037	0.1501	0.0249	0.102	-0.0445	-0.0939	-0.0018	-0.0602	0.0073	0.0522	0.0527	0.0705	0.0671	0.1263	-0.0864	-0.1382	-0.0986	8.763	-5.371	-18.5616
13	0.5521	0.2904	-0.165	0.6856	-0.0904	0.6235	-0.0098	0.0163	-0.2597	-0.0783	0.0316	-0.0557	0.1735	0.0035	0.1016	0.0926	-0.0194	-0.0282	-0.1005	0.0102	0.1078	5.311	-18.9061	-2.1114
14	0.4728	0.0619	-0.1894	0.6283	-0.2556	0.7954	0.0825	-0.1426	-0.1143	0.15	-0.0419	0.0385	0.0239	-0.0025	-0.0238	0.1375	-0.0489	0.047	0.0045	0.0321	0.1117	-6.315	-14.0574	4.1368
15	2.184	-0.0153	0.04	1.7158	-0.3723	2.9099	-0.0233	-0.235	-0.0853	0.0507	0.0697	-0.0291	-0.0454	-0.0274	-0.0475	0.0446	-0.0149	0.0292	0.059	-0.0081	0.1478	-18.0642	-12.5104	-8.1032
16	0.3386	-0.072	0.096	0.1809	0.0002	0.3375	-0.0119	0.1302	-0.0573	-0.0746	-0.0082	0.0539	0.0073	-0.0924	-0.0154	0.1068	0.0006	-0.0024	0.0579	-0.0424	-0.0645	-12.05	-1.0034	-20.5496
17	0.7982	0.3059	0.2971	0.7862	0.1217	0.3281	-0.0715	0.2881	0.1096	-0.0997	0.1413	0.0231	-0.0703	0.0616	-0.009	0.0801	-0.1015	0.0023	0.1926	0.0975	0.3678	68.6312	-20.2794	-63.4258
18	0.2915	0.1503	0.054	0.1219	-0.0144	0.0538	-0.0583	0.1375	0.4684	-0.0225	0.0231	0.1058	-0.1161	0.0057	-0.0081	0.1098	-0.0378	-0.0357	0.1443	0.1309	0.6647	47.2266	-12.7229	-63.3885
19	1.0026	0.1017	0.5549	0.1726	-0.1587	0.8765	-0.0439	-0.14	0.3674	0.0169	-0.019	0.0416	-0.0272	-0.0975	0.0487	0.1129	-0.0205	0.0968	0.1401	-0.0847	0.5008	44.502	-20.5583	-46.5074
20	1.5357	0.0057	-0.0959	0.5646	0.0069	0.7096	0.0052	-0.1626	0.0781	0.204	-0.0134	0.0478	0.0842	-0.0736	-0.0044	0.0942	-0.024	0.0038	0.0936	-0.0117	0.2091	62.3677	-29.5057	-45.016
21	0.4261	-0.094	0.2523	0.5675	0.1861	0.394	-0.0101	-0.0366	0.0596	0.0015	-0.019	0.0493	-0.019	-0.0547	-0.0234	0.0126	0.0225	0.0423	-0.0563	0.0131	0.019	-12.0206	-54.2767	7.7364
22	0.8743	-0.1853	0.1728	0.2148	-0.3034	0.4321	-0.0016	-0.0645	0.1979	0.1655	0.0099	0.0019	-0.1764	-0.0771	-0.0317	0.1372	-0.02	0.0293	0.0063	0.0115	0.0467	-5.627	-49.5956	14.3254
23	0.335	0.0882	-0.1932	0.5051	0.0179	0.5765	0.006	-0.0136	0.1986	0.0591	-0.0414	-0.0727	-0.179	0.0504	-0.0722	0.0602	-0.0901	-0.0232	-0.1254	0.0594	0.1262	10.7823	-45.2615	10.3742
24	0.5766	-0.1034	0.1523	0.6228	-0.5663	0.9861	-0.0227	0.1611	0.113	-0.0439	-0.1466	-0.1422	-0.0354	0.2191	0.1288	0.0964	-0.0115	0.0787	0.1192	0.0828	0.1622	18.8688	-49.7506	-3.9394
25	0.9599	0.7489	0.1053	0.6165	0.3056	1.5368	0.0032	0.0418	-0.0926	0.0436	-0.0314	-0.1945	0.1079	0.1246	0.0216	0.1317	0.0365	0.0763	0.0347	0.0694	0.1156	10.3343	-56.1183	-9.6378
26	0.0959	0.0243	-0.0701	0.129	-0.1025	0.2387	-0.0082	0.0828	-0.0015	-0.111	-0.0096	-0.0482	0.097	0.0312	0.0245	0.0975	0.0115	0.0752	0.0402	0.0797	-0.076	-3.3327	-61.8792	-11.8883
27	1.0051	0.0335	0.4991	0.2752	-0.486	1.3384	0.0152	0.112	0.0086	-0.0333	0.0081	-0.0008	0.0748	0.0598	-0.0097	0.1289	0.0154	0.0703	0.0527	0.0141	0.043	-9.164	-59.7408	0.1831
28	0.3163	-0.0814	-0.1755	0.7421	0.1131	0.2681	-0.0476	-0.0475	-0.1059	0.0953	0.0332	-0.0804	0.072	0.0586	-0.0386	0.0288	0.0661	0.0423	-0.0286	-0.0584	0.1422	17.7774	-60.0808	-46.2864
29	0.4126	0.0634	0.2399	0.808	0.2157	1.0277	-0.0205	0.1175	-0.2427	0.0234	-0.0358	0.1687	0.1124	-0.0758	0.003	0.0766	-0.0212	0.0594	-0.007	-0.0861	0.2181	-4.9222	-65.2107	-51.969
30	0.5233	-0.0788	-0.1806	0.8528	0.1423	0.3734	-0.0273	0.2479	-0.1373	-0.2446	0.048	0.0874	-0.0648	-0.0685	0.0733	0.0934	0.013	0.0379	0.0856	-0.1093	0.0489	10.3748	-50.3424	-65.1282
31	0.3151	0.2037	-0.1916	0.176	-0.0852	0.146	-0.1159	-0.0468	-0.3168	0.003	-0.0678	0.2288	0.1616	-0.0711	-0.025	0.1333	-0.0592	0.1006	0.0796	-0.0477	0.4912	46.7442	-20.7233	7.5405
32	1.8289	0.1052	0.0059	2.2834	-1.7187	1.7829	0.0204	0.1453	-0.2081	-0.0295	-0.0726	0.2656	0.0868	-0.3726	0.0723	0.2077	-0.0481	-0.0356	0.3074	-0.1398	0.4126	39.3265	-15.5136	-12.1771
33	1.6432	-0.1864	-0.1265	0.9337	-0.0452	0.8774	0.0489	0.3168	-0.1374	-0.2707	-0.103	0.063	-0.052	-0.1557	0.0457	0.1545	0.0205	-0.0106	0.1126	-0.0338	0.1762	55.5132	-7.8121	-9.7508

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 7 through 215 )	A	7 - 215
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 216 through 267 )	A	216 - 267
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 268 through 378 )	A	268 - 378
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 7 through 136 )	B	7 - 136
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 137 through 247 )	B	137 - 247
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 248 through 378 )	B	248 - 378
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 7 through 99 )	C	7 - 99
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 100 through 164 )	C	100 - 164
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 165 through 247 )	C	165 - 247
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 248 through 293 )	C	248 - 293
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 294 through 378 )	C	294 - 378
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 7 through 99 )	D	7 - 99
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 100 through 164 )	D	100 - 164
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 165 through 220 )	D	165 - 220
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 221 through 267 )	D	221 - 267
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 268 through 378 )	D	268 - 378
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 7 through 99 )	E	7 - 99
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 100 through 199 )	E	100 - 199
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 200 through 263 )	E	200 - 263
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 264 through 378 )	E	264 - 378
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 7 through 73 )	F	7 - 73
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 74 through 99 )	F	74 - 99
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 100 through 199 )	F	100 - 199
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 200 through 232 )	F	200 - 232
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 233 through 267 )	F	233 - 267
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 268 through 353 )	F	268 - 353
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 354 through 378 )	F	354 - 378
28	X-RAY DIFFRACTION	28	chain 'G' and (resid 7 through 99 )	G	7 - 99
29	X-RAY DIFFRACTION	29	chain 'G' and (resid 100 through 247 )	G	100 - 247
30	X-RAY DIFFRACTION	30	chain 'G' and (resid 248 through 378 )	G	248 - 378
31	X-RAY DIFFRACTION	31	chain 'H' and (resid 7 through 220 )	H	7 - 220
32	X-RAY DIFFRACTION	32	chain 'H' and (resid 221 through 267 )	H	221 - 267
33	X-RAY DIFFRACTION	33	chain 'H' and (resid 268 through 378 )	H	268 - 378

-
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://pdbjlvh1.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