PDB-5o8q: Crystal structure of R. ruber ADH-A, mutant Y294F, W295A

ID or keywords:

Entry

Database: PDB / ID: 5o8q

Title

Crystal structure of R. ruber ADH-A, mutant Y294F, W295A

Components

Alcohol dehydrogenase

Keywords

OXIDOREDUCTASE / alcohol dehydrogenase mutant variant / NADH-dependent / Zn2+-dependent /

Rossmann fold

Function / homology

Function and homology information

oxidoreductase activity / zinc ion binding
Similarity search - Function

Biological species

Rhodococcus sp. M8 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.22 Å

Authors

Dobritzsch, D. / Maurer, D. / Hamnevik, E. / Enugala, T.R. / Widersten, M.

Funding support

Sweden, 1items

Citation

Journal: FEBS J. / Year: 2017
Title: Relaxation of nonproductive binding and increased rate of coenzyme release in an alcohol dehydrogenase increases turnover with a nonpreferred alcohol enantiomer.
Authors: Hamnevik, E. / Enugala, T.R. / Maurer, D. / Ntuku, S. / Oliveira, A. / Dobritzsch, D. / Widersten, M.

History

Deposition	Jun 14, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 11, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim 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_ptnr1_label_alt_id / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5o8q.cif.gz	998.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5o8q.ent.gz	841.2 KB	Display	PDB format
PDBx/mmJSON format	5o8q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o8/5o8q ftp://data.pdbj.org/pub/pdb/validation_reports/o8/5o8q	HTTPS FTP

-
Related structure data

Related structure data	5o8hC 5o9dC 5o9fC 3jv7S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5o8h-d 3pii-d 2xaa-d 1nvg-1 5o9d-d 4cpd-d 5o9f-d 6ffx-d 2ejv-1 3meq-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) 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	#13 - Jan 2001 Alcohol Dehydrogenase similarity (9) #32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: Alcohol dehydrogenase

B: Alcohol dehydrogenase

C: Alcohol dehydrogenase

D: Alcohol dehydrogenase

E: Alcohol dehydrogenase

F: Alcohol dehydrogenase

G: Alcohol dehydrogenase

H: Alcohol dehydrogenase

hetero molecules

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

1

A: Alcohol dehydrogenase

D: Alcohol dehydrogenase

E: Alcohol dehydrogenase

G: Alcohol dehydrogenase

hetero molecules

defined by author&software
Evidence: homology, PISA analysis
147 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Alcohol dehydrogenase

C: Alcohol dehydrogenase

F: Alcohol dehydrogenase

H: Alcohol dehydrogenase

hetero molecules

defined by author&software
Evidence: homology, PISA analysis
147 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	103.689, 109.458, 256.653
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 1 - 345 / Label seq-ID: 1 - 345

NCS ensembles :

#1: Protein	Alcohol dehydrogenase / Mass: 35968.887 Da / Num. of mol.: 8 / Mutation: Y294F, W295A Source method: isolated from a genetically manipulated source Details: contains C-terminal His-tag / Source: (gene. exp.) Rhodococcus sp. M8 (bacteria) / Gene: BKE56_025765 / Plasmid: pGT7ADHA-5H / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: A0A1Q8I6M1
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 752 / 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: 2.49 Å³/Da / Density % sol: 50.3 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 16% PAA, 20mM MgCl2, 0.1 m Tris pH8, 4mM NAD+, 10mM Acetophenone, 7 mg/ml ADH-A

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 18, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.21→29.74 Å / Num. obs: 144348 / % possible obs: 99 % / Redundancy: 7.4 % / B_iso Wilson estimate: 25.9 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.168 / R_pim(I) all: 0.092 / Net I/σ(I): 7.8
Reflection shell	Resolution: 2.21→2.25 Å / Redundancy: 5.9 % / R_merge(I) obs: 0.68 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5774 / CC_1/2: 0.763 / R_pim(I) all: 0.285 / % possible all: 80.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3jv7

3jv7

Resolution: 2.22→29.64 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.938 / SU B: 11.201 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.191 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21576	7306	5.1 %	RANDOM
R_work	0.19351	-	-	-
obs	0.19463	136802	99.26 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 39.583 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.13 Å²	0 Å²	0 Å²
2-	-	0.39 Å²	-0 Å²
3-	-	-	-2.52 Å²

Refinement step

Cycle: 1 / Resolution: 2.22→29.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19705	0	368	752	20825

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	20525
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	19351
X-RAY DIFFRACTION	r_angle_refined_deg	1.426	1.99	28073
X-RAY DIFFRACTION	r_angle_other_deg	0.945	3	44548
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.659	5	2760
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.723	22.769	715
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.63	15	2858
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.857	15	146
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	3303
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	23346
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4112
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.64	1.962	11049
X-RAY DIFFRACTION	r_mcbond_other	0.64	1.962	11048
X-RAY DIFFRACTION	r_mcangle_it	1.13	2.941	13800
X-RAY DIFFRACTION	r_mcangle_other	1.13	2.941	13801
X-RAY DIFFRACTION	r_scbond_it	0.682	2.099	9476
X-RAY DIFFRACTION	r_scbond_other	0.682	2.099	9477
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.164	3.108	14272
X-RAY DIFFRACTION	r_long_range_B_refined	3.416	23.724	20720
X-RAY DIFFRACTION	r_long_range_B_other	3.373	23.574	20613
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	19588	0.05
1	2	B	19588	0.05
2	1	A	19528	0.04
2	2	C	19528	0.04
3	1	A	19552	0.05
3	2	D	19552	0.05
4	1	A	19522	0.05
4	2	E	19522	0.05
5	1	A	19610	0.04
5	2	F	19610	0.04
6	1	A	19558	0.05
6	2	G	19558	0.05
7	1	A	19362	0.06
7	2	H	19362	0.06
8	1	B	19560	0.04
8	2	C	19560	0.04
9	1	B	19614	0.04
9	2	D	19614	0.04
10	1	B	19470	0.05
10	2	E	19470	0.05
11	1	B	19550	0.05
11	2	F	19550	0.05
12	1	B	19524	0.05
12	2	G	19524	0.05
13	1	B	19468	0.05
13	2	H	19468	0.05
14	1	C	19566	0.05
14	2	D	19566	0.05
15	1	C	19640	0.04
15	2	E	19640	0.04
16	1	C	19620	0.04
16	2	F	19620	0.04
17	1	C	19642	0.04
17	2	G	19642	0.04
18	1	C	19478	0.06
18	2	H	19478	0.06
19	1	D	19544	0.04
19	2	E	19544	0.04
20	1	D	19632	0.04
20	2	F	19632	0.04
21	1	D	19632	0.04
21	2	G	19632	0.04
22	1	D	19524	0.05
22	2	H	19524	0.05
23	1	E	19578	0.04
23	2	F	19578	0.04
24	1	E	19660	0.04
24	2	G	19660	0.04
25	1	E	19412	0.05
25	2	H	19412	0.05
26	1	F	19638	0.04
26	2	G	19638	0.04
27	1	F	19470	0.05
27	2	H	19470	0.05
28	1	G	19444	0.05
28	2	H	19444	0.05

LS refinement shell

Resolution: 2.217→2.274 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.274	536	-
R_work	0.266	9100	-
obs	-	-	91.18 %

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	4.7837	-1.4008	0.5028	3.6978	-0.8605	3.1177	0.1978	0.2954	-0.0703	-0.2853	-0.2388	-0.3003	0.3459	0.4962	0.041	0.2073	-0.0513	-0.0307	0.2053	-0.0334	0.2279	6.8688	182.6758	87.4373
2	1.7362	0.7909	0.2893	2.7984	-0.7025	1.2133	-0.0292	-0.0858	0.0143	0.0576	-0.0107	-0.195	-0.0387	0.1986	0.0399	0.0367	-0.0072	0.0127	0.0679	-0.0337	0.0894	-8.6469	170.1111	90.547
3	1.4163	0.5361	0.7646	3.6318	0.8128	1.3854	0.087	-0.1512	-0.0961	0.4289	-0.0342	-0.2486	0.0946	0.2093	-0.0528	0.0759	-0.0105	-0.0024	0.1089	0.0192	0.0536	-6.3887	162.9414	91.8205
4	4.5439	-0.4893	-0.1091	2.4507	-0.5162	2.1565	0.0917	0.1178	-0.07	-0.256	-0.1374	-0.3369	-0.0605	0.4663	0.0457	0.2224	-0.1089	-0.0724	0.2403	-0.0275	0.2191	5.579	182.5678	28.4197
5	1.1185	0.5038	0.2931	2.4853	-0.6024	1.903	-0.0997	-0.0469	0.0732	0.1012	0.0237	-0.159	-0.0988	0.2785	0.076	0.0188	0.0023	-0.0207	0.0617	-0.0108	0.0792	-10.1064	169.6723	29.0522
6	0.8666	0.0458	0.3389	2.6167	0.6931	2.0134	-0.0315	-0.1218	-0.0317	0.3205	-0.0048	-0.1321	0.0905	0.2836	0.0363	0.0424	0.012	-0.0075	0.094	0.0305	0.0578	-8.0124	162.5616	30.7748
7	3.4462	-0.9168	1.0352	2.6282	-0.4493	4.3536	-0.0634	-0.2413	0.3543	-0.0969	0.0214	0.1282	-1.3255	-0.208	0.042	0.7136	-0.121	0.0236	0.191	0.045	0.2799	-18.3863	198.751	-2.477
8	2.01	0.2934	0.6397	1.0046	0.1027	2.6326	-0.0517	0.1384	0.176	-0.1863	-0.0099	-0.0501	-0.4594	0.016	0.0615	0.1204	0.0141	0.0054	0.0236	0.025	0.0694	-26.0544	179.8962	-1.6113
9	3.1187	0.4836	-1.1032	1.0898	-0.5432	2.6571	-0.0052	0.3811	0.1283	-0.1568	0.0509	0.0726	-0.3431	-0.2789	-0.0457	0.1471	0.0481	-0.0312	0.0659	0.0033	0.0242	-33.4365	179.8135	-2.972
10	4.0938	-1.9247	-0.5574	4.42	1.2659	2.787	0.131	0.2395	0.124	-0.3693	-0.2669	0.3267	-0.2111	-0.5204	0.1359	0.1217	-0.0212	0.0011	0.1872	0.0254	0.173	-56.728	151.8682	96.0546
11	0.7264	0.2939	-0.278	2.4611	0.3744	1.1493	-0.0133	-0.0977	-0.0526	0.0717	-0.0429	0.1973	-0.0671	-0.2205	0.0562	0.0137	0.0259	-0.004	0.0834	0.0085	0.0896	-41.2391	164.6024	93.9007
12	0.9595	0.1932	-0.599	1.8822	-0.6385	2.0788	0.0484	-0.0905	0.0816	0.2444	-0.0473	0.1581	-0.272	-0.1838	-0.0012	0.0672	0.0351	-0.0181	0.0734	-0.0452	0.0941	-43.4441	171.849	93.9932
13	3.3467	-1.7532	-1.0184	3.3927	0.7565	3.5814	0.0502	-0.3332	-0.1272	0.0695	0.163	-0.144	0.7317	0.417	-0.2133	0.3185	0.0075	-0.1201	0.1184	-0.0283	0.229	-32.0276	129.2843	69.9594
14	1.8846	0.5498	-0.4352	1.8825	0.0701	1.7585	-0.0046	0.0708	-0.1554	-0.2524	0.0108	-0.0153	0.2142	0.1229	-0.0062	0.0978	0.0234	-0.0428	0.0173	-0.0053	0.0719	-24.8351	147.8861	66.4163
15	3.0282	1.1327	1.1585	2.0116	0.7054	2.0206	0.036	0.4131	-0.124	-0.2862	0.0979	-0.1822	0.1705	0.2905	-0.1339	0.1424	0.0444	0.0206	0.0732	-0.0169	0.0254	-17.4383	147.7764	65.1107
16	3.5403	-0.8822	-0.0648	3.3671	0.5552	3.0693	0.2064	0.3628	0.3004	-0.3795	-0.1428	0.2103	-0.2585	-0.5176	-0.0636	0.1669	-0.0155	0.0606	0.224	0.068	0.198	-58.4516	151.5103	26.4065
17	0.8325	0.5164	-0.3315	2.8044	0.2505	1.2655	-0.0363	0.0141	-0.021	0.1066	-0.0036	0.1751	-0.0017	-0.2352	0.0399	0.0162	0.0114	0.0057	0.0624	0.0163	0.0582	-42.7177	164.2473	26.7907
18	1.0106	0.5062	-0.4918	3.1916	-1.1122	1.8046	0.0701	-0.0418	0.12	0.3845	-0.0303	0.2838	-0.2212	-0.2486	-0.0398	0.0654	0.0278	0.0168	0.0732	-0.036	0.0533	-44.8977	171.4488	26.39
19	5.0266	-2.3046	1.8919	4.4434	0.1761	3.5555	-0.1234	-0.5318	0.7397	-0.411	0.0672	-0.1452	-1.1531	-0.1901	0.0563	0.8402	-0.0389	0.0993	0.2313	0.0737	0.4222	-22.1989	199.4675	60.8206
20	2.7335	0.7192	0.887	1.5449	0.6908	2.8086	-0.0095	0.1564	0.2786	-0.4559	-0.079	-0.0338	-0.6239	0.0442	0.0885	0.2728	0.0519	0.017	0.0327	0.017	0.0839	-28.2602	181.1991	63.3477
21	2.5607	0.0574	-0.9508	1.3739	-0.0203	2.8896	0.0655	0.3314	0.0966	-0.4183	-0.0707	0.1552	-0.512	-0.3699	0.0052	0.3298	0.1256	-0.082	0.0913	-0.0109	0.0567	-38.169	180.1484	62.8207
22	2.4701	-1.422	-1.3517	4.4583	-0.8792	3.2489	0.1736	-0.2611	-0.4136	-0.3074	-0.236	-0.2519	1.0513	0.4796	0.0624	0.8403	-0.0024	-0.0707	0.3515	-0.0684	0.3776	-29.679	128.281	5.1258
23	3.0744	0.6723	-1.1655	1.4181	-0.2637	2.7465	-0.1198	0.12	-0.3188	-0.1985	-0.0065	0.015	0.6224	0.1265	0.1263	0.1851	0.0518	-0.014	0.0462	-0.012	0.0673	-22.3202	147.0051	2.634
24	3.8109	0.4307	1.0421	1.5195	0.5336	2.7077	0.015	0.476	-0.403	-0.1982	0.1032	-0.1033	0.4423	0.3402	-0.1182	0.1795	0.0679	0.0371	0.1065	-0.0216	0.077	-14.4011	146.9913	2.6937

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 82
2	X-RAY DIFFRACTION	2	A	83 - 231
3	X-RAY DIFFRACTION	3	A	232 - 345
4	X-RAY DIFFRACTION	4	B	1 - 82
5	X-RAY DIFFRACTION	5	B	83 - 231
6	X-RAY DIFFRACTION	6	B	232 - 345
7	X-RAY DIFFRACTION	7	C	1 - 82
8	X-RAY DIFFRACTION	8	C	83 - 231
9	X-RAY DIFFRACTION	9	C	232 - 345
10	X-RAY DIFFRACTION	10	D	1 - 82
11	X-RAY DIFFRACTION	11	D	83 - 231
12	X-RAY DIFFRACTION	12	D	232 - 345
13	X-RAY DIFFRACTION	13	E	1 - 82
14	X-RAY DIFFRACTION	14	E	83 - 231
15	X-RAY DIFFRACTION	15	E	232 - 345
16	X-RAY DIFFRACTION	16	F	1 - 82
17	X-RAY DIFFRACTION	17	F	83 - 231
18	X-RAY DIFFRACTION	18	F	232 - 345
19	X-RAY DIFFRACTION	19	G	1 - 82
20	X-RAY DIFFRACTION	20	G	83 - 221
21	X-RAY DIFFRACTION	21	G	222 - 345
22	X-RAY DIFFRACTION	22	H	1 - 79
23	X-RAY DIFFRACTION	23	H	80 - 231
24	X-RAY DIFFRACTION	24	H	232 - 345

-
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