PDB-2omo: Putative antibiotic biosynthesis monooxygenase from Nitrosomonas ...

ID or keywords:

Entry

Database: PDB / ID: 2omo

Title

Putative antibiotic biosynthesis monooxygenase from Nitrosomonas europaea

Components

DUF176

Keywords

OXIDOREDUCTASE / structural genomics / APC6266 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

oxidoreductase activity / cytosol
Similarity search - Function

Biological species

Nitrosomonas europaea (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.83 Å

Authors

Osipiuk, J. / Evdokimova, E. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: X-ray structure of putative antibiotic biosynthesis monooxygenase from Nitrosomonas europaea.
Authors: Osipiuk, J. / Evdokimova, E. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A.

History

Deposition	Jan 22, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 30, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4	Dec 27, 2023	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2omo.cif.gz	197.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2omo.ent.gz	160.9 KB	Display	PDB format
PDBx/mmJSON format	2omo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Similar structure data	1lbu-d 1cvj-3 3dcg-1 2wa2-1 6wn7-2 6scf-3 4pfr-2 3dcg-2 3auv-6 2a90-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC6266

Similar structure data

Other databases

TargetDB: APC6266

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: DUF176

B: DUF176

C: DUF176

D: DUF176

E: DUF176

F: DUF176

G: DUF176

H: DUF176

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

1

A: DUF176

H: DUF176

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

2

B: DUF176

C: DUF176

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

3

D: DUF176

G: DUF176

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

4

E: DUF176

F: DUF176

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

Unit cell

Length a, b, c (Å)	50.155, 99.248, 192.672
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

unknown, putative dimer

#1: Protein	DUF176 / putative antibiotic biosynthesis monooxygenase Mass: 14518.295 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Strain: IFO 14298 / Gene: NE0621 / Plasmid: pET15b modified / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q82WP3
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.06 Å³/Da / Density % sol: 40.4 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Sodium chloride, 0.1 M Bis-Tris buffer, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9797 Å
Detector	Type: SBC-3 / Detector: CCD / Date: Nov 21, 2006
Radiation	Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9797 Å / Relative weight: 1
Reflection	Resolution: 1.83→36.74 Å / Num. all: 82843 / Num. obs: 82843 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.3 % / B_iso Wilson estimate: 35.3 Å² / R_merge(I) obs: 0.094 / Net I/σ(I): 29.7
Reflection shell	Resolution: 1.83→1.91 Å / Redundancy: 7.7 % / R_merge(I) obs: 0.762 / Mean I/σ(I) obs: 2.19 / Num. unique all: 3788 / % possible all: 57.8

-
Processing

Software

Name	Version	Classification
SHELXD		phasing
MLPHARE		phasing
DM		model building
SOLVE		phasing
RESOLVE		model building
HKL-2000		data scaling
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
DM		phasing
RESOLVE		phasing
HKL-3000		phasing
REFMAC	5.2.0019	refinement

Refinement

Method to determine structure:

SAD / Resolution: 1.83→36.74 Å / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2277	4158	5 %	RANDOM
R_work	0.1895	-	-	-
all	0.1914	78518	-	-
obs	0.1914	78518	96.47 %	-

Displacement parameters

B_iso mean: 19.436 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.37 Å²	0 Å²	0 Å²
2-	-	-0.22 Å²	0 Å²
3-	-	-	-0.15 Å²

Refinement step

Cycle: LAST / Resolution: 1.83→36.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6598	0	0	609	7207

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	7028
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.516	1.934	9552
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.014	5	871
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.983	22.584	356
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.663	15	1234
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.287	15	65
X-RAY DIFFRACTION	r_chiral_restr	0.111	0.2	999
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	5439
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.218	0.2	3281
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.308	0.2	4693
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.167	0.2	601
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.258	0.2	90
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.183	0.2	22
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	1.058	1.5	4244
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.485	2	6699
X-RAY DIFFRACTION	r_scbond_it	2.532	3	3229
X-RAY DIFFRACTION	r_scangle_it	3.704	4.5	2817
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.83→1.88 Å

	R_factor	Num. reflection	% reflection
R_free	0.352	185	-
R_work	0.265	-	-
obs	-	3954	63.22 %

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	0.6639	-2.3626	-2.0345	8.8994	5.4256	12.9331	0.2694	-0.4502	-0.1296	-0.0665	-0.3016	0.3917	-0.5162	-0.0055	0.0322	0.0072	-0.0434	-0.0004	0.0773	-0.0533	0.0365	45.556	22.176	26.072
2	1.2195	0.1198	0.2373	3.068	3.0071	2.9592	0.0362	-0.0312	0.0321	-0.2658	0.1488	-0.0907	-0.1966	-0.0256	-0.185	0.0411	-0.0288	-0.0316	0.0539	0.0048	0.0599	37.658	0.768	10.317
3	8.0569	-6.1046	-1.4216	5.8377	-0.4799	2.6297	0.1191	0.1709	-0.1322	-0.1468	-0.0622	0.1141	-0.0814	-0.2645	-0.0569	0.0395	0.0002	-0.0297	0.0719	-0.0146	0.0069	35.513	6.78	5.23
4	0.2936	0.6854	0.3706	1.6204	0.7506	1.1121	0.0402	-0.2114	0.0142	-0.076	-0.1111	0.2177	-0.0006	-0.3137	0.0709	0.0257	0.0034	-0.0134	0.0964	-0.0198	0.0692	30.865	7.195	13.151
5	3.6014	1.9415	1.4712	1.4499	1.671	2.5123	0.0851	0.0732	-0.0203	-0.0012	0.1683	0.2377	0.2612	-0.179	-0.2535	0.0886	-0.0091	-0.0328	0.0952	0.0272	0.1005	38.902	5.551	15.79
6	6.4581	0.5228	1.8298	1.2174	0.0765	0.7309	-0.1275	0.2783	0.2361	-0.0804	0.1355	-0.0086	-0.2029	0.0464	-0.008	0.0221	0.0001	0.0186	0.0587	-0.0801	0.0686	53.722	8.151	-14.067
7	11.2425	9.3402	-1.7673	9.6051	-0.6108	1.3843	-0.1637	0.2302	0.2054	-0.2264	0.1236	0.271	-0.2085	-0.1158	0.0401	0.017	0.0221	0.0129	0.0691	-0.0452	0.0162	38.72	12.017	-27.517
8	0.3684	0.0982	0.0562	1.9022	-0.0361	0.01	0.0127	-0.1216	-0.0968	0.0717	-0.0445	-0.0592	-0.0251	-0.0836	0.0318	-0.0055	-0.0135	0.001	0.0788	-0.0214	0.0741	44.477	8.023	-21.899
9	4.7637	3.9737	0.0744	3.3932	-0.1881	0.7975	0.0943	-0.3344	-0.2435	0.1613	-0.2236	-0.1755	0.075	-0.1965	0.1293	0.0148	0.0263	0.0155	0.1151	-0.0599	0.1204	33.503	14.484	-19.625
10	7.5951	-3.1053	1.7773	1.7692	0.3893	2.9086	0.0838	-0.1312	0.2437	0.0133	0.0075	-0.2418	-0.2764	-0.086	-0.0914	0.0158	0.0003	0.0211	0.0424	-0.0406	0.0551	50.574	6.902	-16.122
11	5.3628	-0.9098	6.9974	1.4954	-1.5288	13.5219	0.2117	-0.1267	-0.1363	-0.1427	0.0841	0.3609	-0.0069	-0.6036	-0.2957	0.0545	0.032	0.0039	0.0777	-0.0421	0.1281	49.011	-2.572	-24.178
12	0.2448	0.4299	1.389	2.9882	-1.5794	15.1103	0.0882	0.1399	-0.0555	-0.0793	-0.0478	-0.1382	0.0195	0.6265	-0.0404	-0.0242	-0.013	0.0203	0.0725	-0.0457	0.0757	64.154	1.29	-25.084
13	0.3938	0.2012	0.4283	0.4317	0.0093	0.5992	0.0643	-0.0073	0.0132	0.0416	0.0174	0.0543	0.0991	0.0354	-0.0817	0.0265	0.0088	-0.0165	0.0792	-0.0247	0.0264	55.152	-0.73	-22.954
14	1.0591	-0.7695	2.8514	0.9548	-2.4049	7.9572	0.2062	-0.0743	-0.0711	0.1492	-0.0456	0.1224	0.1487	-0.1977	-0.1606	0.0462	0.0343	-0.039	0.0636	-0.0503	0.077	64.188	-9.501	-21.968
15	9.2829	-5.2741	5.6719	5.8942	-1.7777	4.1858	0.3118	0.2184	-0.0146	-0.4791	-0.2362	0.0186	0.0179	0.3677	-0.0756	0.0236	-0.0005	0.0215	0.0731	-0.0521	0.0196	47.037	-0.924	-26.8
16	4.6891	-0.5208	-3.7984	14.2193	-9.4211	9.9184	-0.1556	-0.1505	-0.1804	-0.0754	-0.3304	-0.9579	0.9809	0.9748	0.486	0.2165	0.0211	-0.1336	0.2902	-0.0531	0.2031	55.126	-11.985	-44.05
17	8.2994	-0.5221	-0.3564	0.8962	-1.0392	4.8361	0.047	0.4051	0.2561	-0.1004	-0.079	-0.0902	-0.6057	0.2464	0.0319	0.2069	-0.0056	-0.0801	-0.037	-0.0376	-0.0218	43.139	5.144	-58.117
18	0.3328	0.0191	0.9085	0.4909	0.0664	2.4804	-0.0076	0.1364	0.0583	-0.043	-0.0593	0.083	-0.3289	0.1298	0.0669	0.0872	0.0185	-0.0397	0.0174	0.0264	0.0054	45.734	-0.208	-53.626
19	4.712	-5.7899	-4.9622	7.1146	6.0935	5.2673	-0.0454	-0.6156	-0.3536	0.4771	-0.1543	0.0441	-1.032	-0.053	0.1997	0.4161	0.0196	-0.139	0.1063	0.0399	0.056	43.164	12.176	-51.774
20	3.7324	-6.3071	0.9922	14.9951	2.9694	5.2405	0.102	0.0343	0.1071	-0.3159	0.0732	-0.5319	-0.1794	0.4126	-0.1752	0.0698	-0.0249	-0.0348	0.0473	0.0074	-0.0047	48.46	-7.289	-48.489
21	0.9805	2.754	1.1373	8.6111	5.1659	5.7571	0.2583	-0.1656	0.0748	0.448	-0.369	-0.2084	0.837	-0.1323	0.1107	0.2403	-0.0796	0.0088	-0.0054	-0.0081	0.0065	19.965	-27.181	-26.61
22	11.2975	2.3382	-10.5226	3.8217	-5.0751	16.1503	-0.0433	0.4719	-0.1729	-0.2554	-0.216	-0.3239	1.1519	-0.0028	0.2593	0.2691	0.1666	-0.0363	-0.0502	0.0138	0.1583	29.71	-29.125	-25.986
23	5.679	6.2772	-2.2776	9.071	1.5079	8.5116	-0.1575	0.4738	0.633	0.0565	0.2066	0.3745	0.9474	-0.0818	-0.0491	0.1128	0.0436	-0.0612	-0.016	0.0021	-0.017	26.91	-23.446	-22.897
24	0.6976	-2.0705	-2.7181	7.9957	4.9496	15.8434	0.1226	-0.0832	0.2056	-0.4231	0.0617	-0.0202	-0.8262	1.3182	-0.1843	0.0292	-0.0895	0.0681	0.1608	-0.0172	0.0197	33.333	-15.309	-31.006
25	0.7047	1.2164	-0.1387	6.274	6.1466	9.7971	0.1459	-0.0826	0.1674	0.0969	-0.3336	0.2289	0.6291	-0.3908	0.1877	0.1375	0.0181	-0.0302	0.0057	0.0173	0.0635	22.843	-21.178	-29.003
26	3.1685	3.3206	3.0318	14.7108	3.3172	3.5617	0.2967	-0.2242	-0.3667	-0.4181	-0.0766	-0.9269	0.5557	0.2381	-0.22	0.2546	-0.2246	-0.0142	0.1696	0.0899	-0.0191	24.652	-24.223	-9.822
27	1.2228	-2.3043	-0.7161	12.5174	10.0993	10.1341	0.4249	-0.0879	0.6379	-0.7632	-0.297	-0.1948	0.457	-0.4885	-0.1279	0.1722	-0.0878	-0.0688	0.0083	0.0166	0.0326	31.812	-12.185	-1.682
28	9.9918	-0.7887	3.3677	5.7219	-1.0304	16.6759	-0.1118	-0.5601	-0.0961	1.0373	0.0507	-0.7834	0.0599	1.2917	0.061	0.3283	0.0228	-0.0908	0.215	0.0589	0.3536	37.211	-27.523	-6.72
29	0.4297	-0.1211	-0.0431	3.4026	1.5962	0.7492	0.1043	-0.404	-0.2566	1.0782	-0.1641	0.012	0.3993	-0.2689	0.0597	0.413	-0.1208	-0.0927	0.1392	0.0389	0.1834	27.793	-23.066	-3.776
30	1.2214	-1.5571	-2.2693	15.9718	22.4327	31.5134	0.2423	-0.2034	0.1401	0.3216	-0.5595	0.4259	0.8882	-0.0615	0.3172	0.1349	-0.1334	-0.0025	0.0098	-0.0143	0.0185	21.477	-28.238	-12.245
31	3.6241	-0.4741	1.5322	2.454	1.5742	1.9644	-0.0793	0.3061	0.16	-0.0774	-0.0342	0.0289	-0.4233	0.2675	0.1135	0.0643	-0.0119	-0.0603	0.0738	-0.0218	0.0668	39.517	-12.984	-52.78
32	2.8488	1.2459	-0.6258	0.5531	0.0883	16.1005	0.0314	0.119	-0.2485	-0.1159	0.0203	-0.0963	0.7314	0.6481	-0.0517	0.0323	0.0511	-0.0428	0.0936	-0.031	0.051	48.698	-20.357	-54.958
33	0.6471	-0.0387	0.5305	0.0439	-0.2073	1.1769	-0.024	0.0309	0.0635	0.0165	-0.0117	0.0014	0.1091	0.0182	0.0357	0.0648	0.0159	-0.0306	0.0527	0.0063	0.0107	42.152	-14.005	-54.026
34	2.316	-0.7539	0.8441	0.8446	-1.6908	3.6541	0.143	-0.2296	-0.078	0.0793	0.011	0.2577	-0.149	-0.2158	-0.154	0.2154	0.0006	-0.0666	0.0268	0.0221	0.0609	40.104	-26.292	-51.792
35	1.8773	1.6106	1.0113	17.9493	-7.9758	5.2653	-0.3163	0.0732	-0.0595	-0.4986	0.0519	-0.1596	0.1516	-0.0292	0.2644	0.0315	0.046	-0.0388	0.0988	-0.0303	0.0173	36.833	-8.196	-56.423
36	1.3995	0.7671	-0.3656	3.4687	1.3886	2.8444	0.0444	0.0849	0.0381	-0.0976	-0.1193	0.0687	0.0456	-0.0427	0.0749	0.0017	0.0086	0.0208	0.0401	-0.0173	0.0862	53.281	14.915	15.542
37	1.6351	-0.2081	-1.4267	1.4633	-1.3606	6.2815	0.0852	0.0124	0.0653	-0.0449	-0.0676	-0.0762	-0.2316	-0.0265	-0.0176	0.0359	-0.0045	0.0096	0.0231	-0.0263	0.0526	49.741	17.817	11.122
38	1.5643	1.4166	0.4224	3.4284	2.0422	1.3979	0.1277	-0.0661	-0.0275	-0.1761	0.0047	-0.1035	0.0461	0.0832	-0.1324	0.0477	-0.0071	0.0297	0.071	-0.0385	0.0153	54.658	11.491	-1.5
39	1.0936	1.0936	1.1361	1.3363	1.2422	1.2266	0.1379	-0.0207	-0.2109	0.139	0.2421	-0.153	0.2007	0.1955	-0.38	0.0362	-0.0112	0.0295	0.1267	-0.0611	0.1301	61.698	15.996	13.368
40	16.3024	1.0713	2.248	4.3187	3.5874	3.0949	-0.2011	0.7462	0.301	-0.4363	-0.1324	0.143	-0.3843	0.0673	0.3335	0.0723	-0.0087	0.0005	0.0442	-0.0198	0.0521	44.304	4.212	3.395

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	-6 - -2	16 - 20
2	X-RAY DIFFRACTION	2	A	A	-1 - 22	21 - 44
3	X-RAY DIFFRACTION	3	A	A	23 - 47	45 - 69
4	X-RAY DIFFRACTION	4	A	A	48 - 77	70 - 99
5	X-RAY DIFFRACTION	5	A	A	78 - 98	100 - 120
6	X-RAY DIFFRACTION	6	B	B	-6 - 9	16 - 31
7	X-RAY DIFFRACTION	7	B	B	10 - 38	32 - 60
8	X-RAY DIFFRACTION	8	B	B	39 - 65	61 - 87
9	X-RAY DIFFRACTION	9	B	B	66 - 84	88 - 106
10	X-RAY DIFFRACTION	10	B	B	85 - 98	107 - 120
11	X-RAY DIFFRACTION	11	C	C	-5 - 13	17 - 35
12	X-RAY DIFFRACTION	12	C	C	14 - 38	36 - 60
13	X-RAY DIFFRACTION	13	C	C	39 - 65	61 - 87
14	X-RAY DIFFRACTION	14	C	C	66 - 84	88 - 106
15	X-RAY DIFFRACTION	15	C	C	85 - 98	107 - 120
16	X-RAY DIFFRACTION	16	D	D	-6 - 2	16 - 24
17	X-RAY DIFFRACTION	17	D	D	3 - 37	25 - 59
18	X-RAY DIFFRACTION	18	D	D	38 - 65	60 - 87
19	X-RAY DIFFRACTION	19	D	D	66 - 85	88 - 107
20	X-RAY DIFFRACTION	20	D	D	86 - 97	108 - 119
21	X-RAY DIFFRACTION	21	E	E	1 - 22	23 - 44
22	X-RAY DIFFRACTION	22	E	E	23 - 47	45 - 69
23	X-RAY DIFFRACTION	23	E	E	48 - 58	70 - 80
24	X-RAY DIFFRACTION	24	E	E	59 - 67	81 - 89
25	X-RAY DIFFRACTION	25	E	E	68 - 95	90 - 117
26	X-RAY DIFFRACTION	26	F	F	-1 - 12	21 - 34
27	X-RAY DIFFRACTION	27	F	F	13 - 23	35 - 45
28	X-RAY DIFFRACTION	28	F	F	24 - 39	46 - 61
29	X-RAY DIFFRACTION	29	F	F	40 - 85	62 - 107
30	X-RAY DIFFRACTION	30	F	F	86 - 94	108 - 116
31	X-RAY DIFFRACTION	31	G	G	-1 - 12	21 - 34
32	X-RAY DIFFRACTION	32	G	G	13 - 40	35 - 62
33	X-RAY DIFFRACTION	33	G	G	41 - 65	63 - 87
34	X-RAY DIFFRACTION	34	G	G	66 - 84	88 - 106
35	X-RAY DIFFRACTION	35	G	G	85 - 97	107 - 119
36	X-RAY DIFFRACTION	36	H	H	-1 - 21	21 - 43
37	X-RAY DIFFRACTION	37	H	H	22 - 55	44 - 77
38	X-RAY DIFFRACTION	38	H	H	56 - 66	78 - 88
39	X-RAY DIFFRACTION	39	H	H	67 - 87	89 - 109
40	X-RAY DIFFRACTION	40	H	H	88 - 97	110 - 119

-
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