PDB-3gas: Crystal Structure of Helicobacter pylori Heme Oxygenase Hugz in C...

ID or keywords:

Entry

Database: PDB / ID: 3gas

Title

Crystal Structure of Helicobacter pylori Heme Oxygenase Hugz in Complex with Heme

Components

heme oxygenase

Keywords

OXIDOREDUCTASE / heme oxygenase / FMN-binding split barrel

Function / homology

Function and homology information

coenzyme F420 binding / oxidoreductase activity, acting on the CH-CH group of donors / metal ion binding / cytosol
Similarity search - Function

Biological species

Helicobacter pylori (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.8 Å

Authors

Jiang, F. / Hu, Y.L. / Guo, Y. / Guo, G. / Zou, Q.M. / Wang, D.C.

Citation

Journal: To be Published
Title: Crystal Structure of Helicobacter pylori Heme Oxygenase Hugz in Complex with Heme
Authors: Jiang, F. / Hu, Y.L. / Guo, Y. / Guo, G. / Zou, Q.M. / Wang, D.C.

History

Deposition	Feb 18, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 23, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3gas.cif.gz	343.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3gas.ent.gz	276.8 KB	Display	PDB format
PDBx/mmJSON format	3gas.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ga/3gas ftp://data.pdbj.org/pub/pdb/validation_reports/ga/3gas	HTTPS FTP

-
Related structure data

Similar structure data	2op0-d 3lsy-d 2nq8-d 4oqq-d 2op1-d 2ol4-d 1zxl-d 4wl2-3 3swj-2 1oxl-2 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

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: heme oxygenase

B: heme oxygenase

C: heme oxygenase

D: heme oxygenase

E: heme oxygenase

F: heme oxygenase

hetero molecules

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

1

A: heme oxygenase

B: heme oxygenase

hetero molecules

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

2

C: heme oxygenase

D: heme oxygenase

hetero molecules

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

3

E: heme oxygenase

F: heme oxygenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	88.330, 139.340, 152.900
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	heme oxygenase Mass: 29863.961 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: NCTC11639 / Gene: HugZ / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: C0LU01, heme oxygenase (biliverdin-producing)
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-AZI / AZIDE ION Mass: 42.020 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: N₃
#4: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1289 / 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: 2.63 Å³/Da / Density % sol: 53.15 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 3350, tacsimate, imidazole, methanol, pH 7.5, vapor diffusion, hanging drop, temperature 293K

-
Data collection

Diffraction

Mean temperature: 95 K

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: BL-17A / Wavelength: 1.00000, 0.97912, 0.97931, 0.96408

Detector

Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 26, 2008

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1	1
2	0.97912	1
3	0.97931	1
4	0.96408	1

Reflection

Redundancy: 9.9 % / Av σ(I) over netI: 7.8 / Number: 810953 / R_merge(I) obs: 0.06 / R_sym value: 0.06 / D res high: 2.321 Å / D res low: 103.142 Å / Num. obs: 82219 / % possible obs: 100

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Redundancy
7.34	57.83	99.7	1	0.057	0.057	8.9
5.19	7.34	100	1	0.052	0.052	9.6
4.24	5.19	100	1	0.049	0.049	9.8
3.67	4.24	100	1	0.05	0.05	9.9
3.28	3.67	100	1	0.054	0.054	10
3	3.28	100	1	0.059	0.059	10
2.77	3	100	1	0.073	0.073	10
2.59	2.77	100	1	0.088	0.088	10
2.45	2.59	100	1	0.11	0.11	9.9
2.32	2.45	100	1	0.127	0.127	9.7

Reflection

Resolution: 1.8→47.87 Å / Num. all: 165619 / Num. obs: 165702 / % possible obs: 94.9 % / Observed criterion σ(F): 2 / Redundancy: 6.7 % / B_iso Wilson estimate: 20 Å² / Limit h max: 48 / Limit h min: 0 / Limit k max: 74 / Limit k min: 0 / Limit l max: 76 / Limit l min: 0 / Observed criterion F max: 3093830.4 / Observed criterion F min: 4.1 / R_merge(I) obs: 0.049 / R_sym value: 0.049 / Net I/σ(I): 8.621

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.8-1.9	4.5	0.172	4.3	81539	18209	0.172	72.8
1.9-2.01	5.4	0.128	5.5	119174	21917	0.128	91.9
2.01-2.15	7.2	0.119	5.7	161041	22494	0.119	99.9
2.15-2.32	7.3	0.09	7.4	152948	21077	0.09	100
2.32-2.55	7.3	0.067	9.6	142096	19347	0.067	100
2.55-2.85	7.4	0.05	12.1	130521	17599	0.05	100
2.85-3.29	7.5	0.041	13.4	116066	15563	0.041	100
3.29-4.02	7.4	0.038	14.4	98565	13270	0.038	100
4.02-5.69	7.3	0.039	14.2	75570	10341	0.039	100
5.69-47.89	6.8	0.047	10.4	40213	5885	0.047	99.5

-
Phasing

Phasing

Method:

MAD

Phasing MAD set

ID	Highest resolution (Å)	Lowest resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	2.32	57.81	0	0	75375	6758
ISO_2	2.32	57.81	0.596	0.421	74189	6719
ISO_3	2.32	57.81	1.111	0.793	74263	6702
ANO_1	2.32	57.81	1.848	0	75372	0
ANO_2	2.32	57.81	1.368	0	74163	0
ANO_3	2.32	57.81	1.228	0	74223	0

Phasing MAD set shell

ID	Resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	10.22-57.81	0	0	751	316
ISO_1	7.28-10.22	0	0	1452	335
ISO_1	5.96-7.28	0	0	1944	337
ISO_1	5.17-5.96	0	0	2297	334
ISO_1	4.63-5.17	0	0	2642	341
ISO_1	4.23-4.63	0	0	2930	337
ISO_1	3.92-4.23	0	0	3216	348
ISO_1	3.66-3.92	0	0	3443	332
ISO_1	3.46-3.66	0	0	3701	347
ISO_1	3.28-3.46	0	0	3886	338
ISO_1	3.13-3.28	0	0	4129	340
ISO_1	2.99-3.13	0	0	4299	344
ISO_1	2.88-2.99	0	0	4519	338
ISO_1	2.77-2.88	0	0	4681	338
ISO_1	2.68-2.77	0	0	4837	336
ISO_1	2.59-2.68	0	0	5035	342
ISO_1	2.52-2.59	0	0	5215	348
ISO_1	2.45-2.52	0	0	5345	340
ISO_1	2.38-2.45	0	0	5533	344
ISO_1	2.32-2.38	0	0	5520	323
ANO_1	10.22-57.81	0.8	0	751	0
ANO_1	7.28-10.22	2.197	0	1452	0
ANO_1	5.96-7.28	3.688	0	1944	0
ANO_1	5.17-5.96	3.133	0	2297	0
ANO_1	4.63-5.17	2.641	0	2642	0
ANO_1	4.23-4.63	2.374	0	2930	0
ANO_1	3.92-4.23	2.291	0	3216	0
ANO_1	3.66-3.92	2.143	0	3443	0
ANO_1	3.46-3.66	2.094	0	3701	0
ANO_1	3.28-3.46	2.105	0	3886	0
ANO_1	3.13-3.28	2.205	0	4129	0
ANO_1	2.99-3.13	2.161	0	4299	0
ANO_1	2.88-2.99	2.114	0	4519	0
ANO_1	2.77-2.88	1.947	0	4681	0
ANO_1	2.68-2.77	1.707	0	4837	0
ANO_1	2.59-2.68	1.654	0	5035	0
ANO_1	2.52-2.59	1.559	0	5215	0
ANO_1	2.45-2.52	1.394	0	5343	0
ANO_1	2.38-2.45	1.219	0	5533	0
ANO_1	2.32-2.38	1.112	0	5519	0
ISO_2	10.22-57.81	0.473	0.497	749	285
ISO_2	7.28-10.22	0.685	0.616	1442	332
ISO_2	5.96-7.28	1.05	0.379	1925	337
ISO_2	5.17-5.96	0.893	0.651	2268	334
ISO_2	4.63-5.17	0.777	0.635	2616	341
ISO_2	4.23-4.63	0.697	0.476	2894	337
ISO_2	3.92-4.23	0.698	0.475	3177	348
ISO_2	3.66-3.92	0.664	0.474	3396	332
ISO_2	3.46-3.66	0.64	0.438	3651	347
ISO_2	3.28-3.46	0.653	0.386	3835	338
ISO_2	3.13-3.28	0.685	0.414	4068	340
ISO_2	2.99-3.13	0.668	0.413	4234	344
ISO_2	2.88-2.99	0.627	0.382	4446	338
ISO_2	2.77-2.88	0.586	0.369	4610	338
ISO_2	2.68-2.77	0.527	0.329	4753	336
ISO_2	2.59-2.68	0.497	0.304	4942	341
ISO_2	2.52-2.59	0.47	0.315	5123	348
ISO_2	2.45-2.52	0.42	0.252	5244	340
ISO_2	2.38-2.45	0.379	0.26	5418	342
ISO_2	2.32-2.38	0.337	0.235	5398	321
ANO_2	10.22-57.81	0.953	0	749	0
ANO_2	7.28-10.22	1.924	0	1439	0
ANO_2	5.96-7.28	2.648	0	1921	0
ANO_2	5.17-5.96	2.19	0	2264	0
ANO_2	4.63-5.17	1.85	0	2614	0
ANO_2	4.23-4.63	1.741	0	2892	0
ANO_2	3.92-4.23	1.673	0	3175	0
ANO_2	3.66-3.92	1.472	0	3396	0
ANO_2	3.46-3.66	1.483	0	3649	0
ANO_2	3.28-3.46	1.479	0	3832	0
ANO_2	3.13-3.28	1.509	0	4068	0
ANO_2	2.99-3.13	1.475	0	4230	0
ANO_2	2.88-2.99	1.413	0	4445	0
ANO_2	2.77-2.88	1.309	0	4607	0
ANO_2	2.68-2.77	1.17	0	4751	0
ANO_2	2.59-2.68	1.101	0	4934	0
ANO_2	2.52-2.59	1.06	0	5113	0
ANO_2	2.45-2.52	0.958	0	5231	0
ANO_2	2.38-2.45	0.86	0	5400	0
ANO_2	2.32-2.38	0.804	0	5453	0
ISO_3	10.22-57.81	0.982	0.941	747	283
ISO_3	7.28-10.22	1.654	1.078	1439	331
ISO_3	5.96-7.28	1.846	0.766	1931	337
ISO_3	5.17-5.96	1.632	1.11	2270	334
ISO_3	4.63-5.17	1.395	1.056	2618	341
ISO_3	4.23-4.63	1.295	0.852	2898	337
ISO_3	3.92-4.23	1.289	0.913	3182	348
ISO_3	3.66-3.92	1.228	0.913	3397	332
ISO_3	3.46-3.66	1.19	0.784	3655	347
ISO_3	3.28-3.46	1.228	0.838	3834	338
ISO_3	3.13-3.28	1.236	0.805	4074	340
ISO_3	2.99-3.13	1.196	0.786	4239	344
ISO_3	2.88-2.99	1.123	0.74	4454	338
ISO_3	2.77-2.88	1.05	0.7	4611	338
ISO_3	2.68-2.77	0.956	0.631	4756	335
ISO_3	2.59-2.68	0.905	0.567	4954	342
ISO_3	2.52-2.59	0.859	0.569	5128	342
ISO_3	2.45-2.52	0.77	0.445	5251	336
ISO_3	2.38-2.45	0.712	0.511	5429	343
ISO_3	2.32-2.38	0.636	0.433	5396	316
ANO_3	10.22-57.81	0.943	0	747	0
ANO_3	7.28-10.22	1.952	0	1436	0
ANO_3	5.96-7.28	2.523	0	1927	0
ANO_3	5.17-5.96	2.136	0	2266	0
ANO_3	4.63-5.17	1.773	0	2616	0
ANO_3	4.23-4.63	1.617	0	2896	0
ANO_3	3.92-4.23	1.574	0	3180	0
ANO_3	3.66-3.92	1.411	0	3397	0
ANO_3	3.46-3.66	1.307	0	3653	0
ANO_3	3.28-3.46	1.391	0	3831	0
ANO_3	3.13-3.28	1.385	0	4074	0
ANO_3	2.99-3.13	1.303	0	4235	0
ANO_3	2.88-2.99	1.268	0	4448	0
ANO_3	2.77-2.88	1.146	0	4605	0
ANO_3	2.68-2.77	1.004	0	4747	0
ANO_3	2.59-2.68	0.959	0	4950	0
ANO_3	2.52-2.59	0.909	0	5122	0
ANO_3	2.45-2.52	0.811	0	5239	0
ANO_3	2.38-2.45	0.728	0	5417	0
ANO_3	2.32-2.38	0.676	0	5437	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	64.039	35.525	13.718	SE	15.75	0.77
2	56.164	30.749	9.633	SE	15.11	0.77
3	100.044	33.922	85.066	SE	17.65	0.74
4	101.508	35.731	33.006	SE	16.19	0.72
5	107.294	39.122	89.798	SE	18.31	0.74
6	101.435	30.634	41.762	SE	17.34	0.71
7	63.363	15.096	16.029	SE	19.89	0.74
8	66.152	54.328	17.273	SE	22.32	0.77
9	103.04	15.153	32.038	SE	19.99	0.72
10	104.315	54.513	30.08	SE	21.71	0.73
11	52.775	11.763	8.962	SE	22.86	0.78
12	101.873	11.512	44.641	SE	23.12	0.74
13	97.582	54.358	86.339	SE	20.23	0.7
14	96.641	14.987	85.455	SE	25.33	0.77
15	54.253	51.06	12.693	SE	22.84	0.73
16	106.335	18.834	93.525	SE	23.58	0.72
17	108.756	58.249	92.041	SE	25.35	0.74
18	106.047	50.701	42.545	SE	24.61	0.72
19	33.923	55.195	15.424	SE	27.89	0.7
20	113.943	14.71	112.605	SE	31.43	0.71
21	29.532	59.998	15.295	SE	31.55	0.68
22	116.436	9.938	116.427	SE	30.09	0.65
23	33.898	5.525	15.397	SE	37.61	0.68
24	77.301	60.955	95.78	SE	41.4	0.73
25	64.922	8.807	37.648	SE	39.53	0.66
26	77.021	9.278	90.037	SE	35.56	0.61
27	32.281	9.981	20.11	SE	46.58	0.73
28	72.266	65.093	95.011	SE	38.69	0.65
29	68.067	4.596	41.515	SE	35.98	0.61
30	74.89	14.123	93.974	SE	39.55	0.61
31	69.179	49.301	18.213	SE	15.88	0.26
32	103.376	49.666	26.92	SE	16.99	0.24
33	101.809	16.664	47.985	SE	17.45	0.22
34	49.962	17	7.426	SE	22.63	0.26
35	111.683	53.294	93.747	SE	18.63	0.21
36	94.103	19.982	83.197	SE	18.66	0.24

Phasing dm

FOM : 0.85 / FOM acentric: 0.84 / FOM centric: 0.9 / Reflection: 82266 / Reflection acentric: 75488 / Reflection centric: 6778

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
6.6-57.806	1.31	0.99	2.48	3769	2966	803
4.1-6.6	0.95	0.96	0.85	11141	9846	1295
3.3-4.1	0.94	0.95	0.83	13810	12603	1207
2.9-3.3	0.88	0.89	0.71	13852	12832	1020
2.5-2.9	0.78	0.79	0.57	24554	22978	1576
2.3-2.5	0.67	0.68	0.45	15140	14263	877

-
Processing

Software

Name	Version	Classification
SCALA	3.2.25	data scaling
SHARP		phasing
RESOLVE	2.13	phasing
CNS	1.2	refinement
PDB_EXTRACT	3.006	data extraction
ADSC	Quantum	data collection
HKL-2000		data reduction

Refinement

Method to determine structure:

MAD / Resolution: 1.8→47.87 Å / R_factor R_free error: 0.002 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 3093830 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.222	8291	5 %	RANDOM
R_work	0.192	-	-	-
all	-	174565	-	-
obs	-	165278	94.6 %	-

Solvent computation

Solvent model: FLAT MODEL / B_sol: 48.599 Å² / k_sol: 0.4 e/Å³

Displacement parameters

B_iso max: 74.03 Å² / B_iso mean: 26.662 Å² / B_iso min: 6.8 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.89 Å²	0 Å²	0 Å²
2-	-	-3.32 Å²	0 Å²
3-	-	-	-0.57 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.23 Å	0.2 Å
Luzzati d res low	-	5 Å
Luzzati sigma a	0.13 Å	0.09 Å
Luzzati d res high	-	1.8

Refinement step

Cycle: LAST / Resolution: 1.8→47.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11844	0	364	1289	13497

Refine LS restraints

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	c_bond_d	0.01
X-RAY DIFFRACTION	c_angle_deg	1.5
X-RAY DIFFRACTION	c_dihedral_angle_d	22.9
X-RAY DIFFRACTION	c_improper_angle_d	0.89
X-RAY DIFFRACTION	c_mcbond_it
X-RAY DIFFRACTION	c_mcangle_it
X-RAY DIFFRACTION	c_scbond_it
X-RAY DIFFRACTION	c_scangle_it

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	R_factor R_free	Num. reflection R_free	% reflection R_free (%)	R_factor R_work	Num. reflection R_work	R_factor R_free error	Num. reflection all	Num. reflection obs	% reflection obs (%)
1.8-1.88	0.252	783	5.2	0.221	14398	0.009	21628	15181	70.2
1.88-1.98	0.235	968	5.1	0.199	17966	0.008	21636	18934	87.5
1.98-2.11	0.243	1077	5	0.199	20439	0.007	21739	21516	99
2.11-2.27	0.245	1050	4.8	0.199	20624	0.008	21720	21674	99.8
2.27-2.5	0.232	1060	4.9	0.19	20674	0.007	21770	21734	99.8
2.5-2.86	0.236	1124	5.2	0.199	20670	0.007	21806	21794	99.9
2.86-3.6	0.228	1115	5.1	0.2	20838	0.007	21963	21953	100
3.6-47.87	0.193	1114	5	0.178	21378	0.006	22532	22492	99.8

Xplor file

Refine-ID	Serial no	Param file	Topol file
X-RAY DIFFRACTION	1	protein_rep.param	protein.top
X-RAY DIFFRACTION	2	water_rep.param	water.top
X-RAY DIFFRACTION	3	hem.param	azi.top
X-RAY DIFFRACTION	4	azi.param	hem.top
X-RAY DIFFRACTION	5	edo.param	edo.top

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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