PDB-4q3o: Crystal structure of MGS-MT1, an alpha/beta hydrolase enzyme from...

ID or keywords:

Entry

Database: PDB / ID: 4q3o

Title

Crystal structure of MGS-MT1, an alpha/beta hydrolase enzyme from a Lake Matapan deep-sea metagenome library

Components

MGS-MT1

Keywords

HYDROLASE / metagenome / metagenomic library / alpha and beta proteins / alpha/beta hydrolase superfamily / esterase/lipase fold

Function / homology

Function and homology information

triacylglycerol lipase activity
Similarity search - Function

Biological species

unidentified (others)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.74 Å

Authors

Stogios, P.J. / Xu, X. / Cui, H. / Alcaide, M. / Ferrer, M. / Savchenko, A.

Citation

Journal: Environ Microbiol / Year: 2015
Title: Pressure adaptation is linked to thermal adaptation in salt-saturated marine habitats.
Authors: Alcaide, M. / Stogios, P.J. / Lafraya, A. / Tchigvintsev, A. / Flick, R. / Bargiela, R. / Chernikova, T.N. / Reva, O.N. / Hai, T. / Leggewie, C.C. / Katzke, N. / La Cono, V. / Matesanz, R. / ...

History

Deposition	Apr 11, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 4, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 18, 2015	Group: Database references
Revision 1.2	Sep 20, 2023	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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	4q3o.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb4q3o.ent.gz	868 KB	Display	PDB format
PDBx/mmJSON format	4q3o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q3/4q3o ftp://data.pdbj.org/pub/pdb/validation_reports/q3/4q3o	HTTPS FTP

-
Related structure data

Related structure data	4q3kC 4q3lC 4q3mC 4q3nC 3fakS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4e5s-1 3agc-d 4h1h-d 4y5s-d 1hfb-4 3ioi-1 4y5t-d 4q05-d 1ofb-d 1of6-4 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

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: MGS-MT1

B: MGS-MT1

C: MGS-MT1

D: MGS-MT1

E: MGS-MT1

F: MGS-MT1

G: MGS-MT1

H: MGS-MT1

hetero molecules

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

1

A: MGS-MT1

B: MGS-MT1

hetero molecules

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

2

C: MGS-MT1

F: MGS-MT1

hetero molecules

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

3

D: MGS-MT1

G: MGS-MT1

hetero molecules

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

4

E: MGS-MT1

H: MGS-MT1

hetero molecules

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

Unit cell

Length a, b, c (Å)	189.454, 131.397, 112.441
Angle α, β, γ (deg.)	90.00, 103.55, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-569- HOH
2	1	A-700- HOH
3	1	H-714- HOH

#1: Protein	MGS-MT1 Mass: 38439.945 Da / Num. of mol.: 8 / Fragment: MGS-MT1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Gene: MGS-MT1 / Plasmid: p15Tv-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: A0A0B5KQQ5*PLUS
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3085 / Source method: isolated from a natural source / Formula: H₂O
Source details	The sample has been obtained from Lake Matapan deep-sea and identified using the technique metagenome library

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 44.4 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M MES, 20% PEG10K. Cryroprotectant: 12% Glycerol then paraton-N oil, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 10, 2013
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.74→19.72 Å / Num. obs: 272067 / Observed criterion σ(F): -2 / Observed criterion σ(I): 0 / Redundancy: 3 % / R_merge(I) obs: 0.056 / Net I/σ(I): 21.3
Reflection shell	Resolution: 1.74→1.83 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.392 / Mean I/σ(I) obs: 2.2

-
Processing

Software

Name	Version	Classification
StructureStudio		data collection
PHENIX	(phenix.phaser)	model building
PHENIX	(phenix.refine: 1.9pre_1669)	refinement
XDS		data reduction
SCALA		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3FAK

3fak

Resolution: 1.74→19.72 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 18.2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1852	13720	5.05 %
R_work	0.1452	-	-
obs	0.1472	271731	99.55 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.74→19.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19746	0	232	3085	23063

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	20641
X-RAY DIFFRACTION	f_angle_d	1.482	28138
X-RAY DIFFRACTION	f_dihedral_angle_d	14.074	7600
X-RAY DIFFRACTION	f_chiral_restr	0.083	3172
X-RAY DIFFRACTION	f_plane_restr	0.008	3572

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.74-1.7598	0.2505	462	0.2028	8611	X-RAY DIFFRACTION	100
1.7598-1.7804	0.253	448	0.2	8621	X-RAY DIFFRACTION	100
1.7804-1.8021	0.2292	471	0.1883	8637	X-RAY DIFFRACTION	100
1.8021-1.8249	0.2256	437	0.1839	8608	X-RAY DIFFRACTION	100
1.8249-1.8489	0.2414	500	0.1819	8557	X-RAY DIFFRACTION	100
1.8489-1.8743	0.234	453	0.1833	8655	X-RAY DIFFRACTION	100
1.8743-1.901	0.2354	440	0.1822	8600	X-RAY DIFFRACTION	100
1.901-1.9294	0.2335	465	0.1903	8599	X-RAY DIFFRACTION	100
1.9294-1.9595	0.215	491	0.1637	8553	X-RAY DIFFRACTION	100
1.9595-1.9916	0.1912	432	0.1512	8631	X-RAY DIFFRACTION	100
1.9916-2.0259	0.1913	485	0.1469	8625	X-RAY DIFFRACTION	100
2.0259-2.0627	0.199	451	0.1555	8617	X-RAY DIFFRACTION	100
2.0627-2.1023	0.1958	451	0.1483	8591	X-RAY DIFFRACTION	100
2.1023-2.1452	0.1876	459	0.1343	8598	X-RAY DIFFRACTION	100
2.1452-2.1918	0.1702	453	0.1336	8660	X-RAY DIFFRACTION	100
2.1918-2.2427	0.1962	447	0.1456	8597	X-RAY DIFFRACTION	100
2.2427-2.2987	0.2257	449	0.1582	8667	X-RAY DIFFRACTION	100
2.2987-2.3607	0.1784	484	0.1343	8539	X-RAY DIFFRACTION	100
2.3607-2.4301	0.172	469	0.1336	8648	X-RAY DIFFRACTION	100
2.4301-2.5084	0.1915	440	0.1331	8675	X-RAY DIFFRACTION	100
2.5084-2.5978	0.1911	470	0.1374	8578	X-RAY DIFFRACTION	100
2.5978-2.7016	0.1869	458	0.1385	8657	X-RAY DIFFRACTION	100
2.7016-2.8242	0.1833	463	0.1313	8633	X-RAY DIFFRACTION	100
2.8242-2.9726	0.1747	459	0.1369	8673	X-RAY DIFFRACTION	100
2.9726-3.1582	0.1782	429	0.1369	8640	X-RAY DIFFRACTION	100
3.1582-3.4009	0.1661	471	0.1315	8638	X-RAY DIFFRACTION	100
3.4009-3.741	0.15	442	0.1238	8620	X-RAY DIFFRACTION	99
3.741-4.2775	0.152	443	0.1197	8566	X-RAY DIFFRACTION	99
4.2775-5.3712	0.1558	458	0.1356	8454	X-RAY DIFFRACTION	97
5.3712-19.7249	0.2043	440	0.1853	8263	X-RAY DIFFRACTION	94

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	2.8078	-1.2582	-1.4264	3.8453	5.1896	7.1632	0.0802	-0.2993	-0.4747	0.4954	-0.3131	0.2445	1.0117	-0.4626	0.1961	0.367	-0.0649	0.0195	0.2256	0.1037	0.2127	27.3325	-23.0825	25.7834
2	2.4658	-0.3317	0.2465	2.4047	0.5588	1.8751	-0.0695	-0.02	0.0295	0.0545	-0.0098	0.185	0.0488	-0.3079	0.0519	0.0654	-0.0304	0.0027	0.174	0.0013	0.1402	12.1756	-10.7277	6.593
3	0.9946	-0.0377	0.262	0.7731	0.0595	1.1531	0.0002	-0.0025	0.0149	0.013	0.0273	0.0265	0.0604	-0.062	-0.0226	0.0604	-0.0175	0.0044	0.0832	0.0056	0.0889	29.2352	-11.4978	8.2625
4	7.4549	1.9792	-5.9674	6.5248	-4.9272	8.0008	-0.1506	-0.4618	0.5574	0.4082	-0.1037	-0.1289	-0.6497	0.2007	0.1469	0.2152	0.0352	-0.0762	0.1587	-0.1029	0.2159	22.2919	4.975	15.3028
5	7.8084	1.5658	1.7652	9.0047	-2.186	5.8965	0.1701	-0.3152	-0.5061	0.4826	-0.1146	-0.2443	0.4345	0.2696	0.012	0.1881	0.0472	0.0149	0.1297	-0.0236	0.1374	51.2308	-17.8977	10.3426
6	4.4225	4.9061	3.91	6.0955	4.5402	3.553	0.0056	-0.1412	-0.2221	-0.1858	-0.0046	-0.1232	-0.0318	-0.1018	0.0669	0.1491	0.0164	0.0008	0.1108	0.003	0.1504	57.391	-20.5766	34.5862
7	0.5944	1.3356	-1.1427	7.613	-6.7644	5.9697	-0.0188	0.0359	-0.1326	-0.0007	-0.1339	-0.3411	0.0757	0.1778	0.2772	0.125	0.025	-0.0498	0.1185	-0.0338	0.2025	66.6093	-5.9475	26.2656
8	0.8657	0.3041	0.0975	0.6308	0.0443	0.7134	-0.0021	-0.0783	0.0986	0.0673	-0.0219	0.039	-0.0965	-0.0498	0.0162	0.0973	0.0139	-0.006	0.0754	-0.021	0.0836	49.1078	2.2171	25.9104
9	7.9831	2.3953	-0.1831	8.6636	1.0563	4.649	0.0282	-0.48	-0.3523	0.4356	-0.096	-0.3066	0.3744	0.331	0.05	0.119	0.028	0.0306	0.1436	-0.0107	0.1154	17.5195	-50.2268	-44.4056
10	3.6752	4.8815	4.3325	7.0703	5.9089	5.1446	-0.0181	-0.0631	-0.1887	-0.204	0.1013	-0.3452	0.08	0.0549	-0.088	0.189	0.0519	0.017	0.1572	-0.0076	0.2076	21.3237	-55.4539	-21.3948
11	0.1448	0.5333	-0.5294	7.0555	-6.7078	6.318	-0.1289	-0.0275	-0.1112	0.2037	-0.1795	-0.6146	-0.1777	0.2258	0.4256	0.1432	0.0289	-0.0407	0.1431	-0.0449	0.2416	30.7293	-38.8408	-27.6899
12	0.8182	0.2218	0.1326	0.6922	-0.0361	0.9536	-0.0275	-0.1349	0.1059	0.1225	-0.0083	0.0015	-0.1281	-0.0919	0.014	0.1168	0.0362	-0.0049	0.1051	-0.0396	0.1014	12.9913	-31.8589	-27.82
13	7.0013	0.4213	-0.9198	8.8552	-2.747	7.9724	-0.0641	-0.2989	-0.4657	0.4624	-0.086	-0.2776	0.452	0.4638	0.0809	0.1782	0.0518	-0.0101	0.1124	-0.0326	0.2077	18.276	15.9307	-44.7719
14	0.0424	0.1819	-0.1062	3.0435	-2.8204	2.6148	0.0161	-0.0401	-0.1268	-0.03	-0.0632	-0.1153	0.0472	0.1105	0.084	0.1504	0.0362	-0.0074	0.1127	0.0031	0.2171	30.2358	22.7772	-27.2957
15	0.9784	0.4257	0.3012	0.6495	0.0068	0.7262	0.0545	-0.1729	0.049	0.0829	-0.07	0.0679	-0.0244	-0.1058	0.0072	0.1047	0.0024	-0.0019	0.095	-0.016	0.097	15.1233	34.2089	-26.5154
16	4.1339	-3.3658	-1.7029	5.4481	2.8553	3.9165	0.0615	0.1703	0.127	-0.1648	-0.1287	-0.0403	-0.1473	-0.1783	0.0569	0.0929	-0.0281	-0.0324	0.0598	0.0047	0.1177	14.2726	35.1487	-42.0051
17	8.3786	-0.2731	-0.7737	7.1867	3.9194	8.8409	-0.1392	0.3331	-0.3299	-0.2826	-0.101	0.2435	0.5083	-0.2938	0.1758	0.177	-0.023	0.0367	0.1214	0.0315	0.0982	42.2824	-17.0279	-9.4698
18	5.5945	-3.0318	5.4924	4.5036	-4.9096	8.0762	0.351	-0.0521	-0.2273	0.1898	-0.0626	0.2264	0.1358	0.0437	-0.2352	0.2773	-0.0486	0.0049	0.2129	-0.0346	0.3005	36.8598	-22.4827	-32.3477
19	0.4336	-0.1585	-0.1145	6.2474	2.2896	1.9741	-0.0721	0.0216	-0.1375	-0.1809	-0.133	0.4051	0.0177	-0.1857	0.3254	0.0568	-0.0234	-0.0203	0.1088	0.0173	0.2231	28.9605	-5.7032	-26.7958
20	0.8019	-0.2514	0.0345	0.8966	0.1325	1.2083	0.0143	0.1571	0.1009	-0.1416	-0.0274	-0.0101	-0.0882	0.1603	-0.0011	0.1107	-0.0224	-0.0004	0.1303	0.0378	0.0943	47.2348	0.2607	-27.2975
21	1.2282	-1.6989	-2.2173	4.9817	6.2082	8.0456	-0.0281	-0.2089	-0.3925	0.5963	-0.1723	0.2314	0.9568	-0.535	0.2666	0.3254	-0.0536	0.0476	0.3297	0.0845	0.211	-7.4628	-57.5098	-29.2331
22	7.3712	-1.9179	-3.6138	7.4225	5.3129	7.91	0.1273	-0.0899	-0.9735	0.4019	0.2408	0.0352	0.2669	-0.3332	-0.0929	0.2373	-0.0611	0.0198	0.4186	0.1969	0.4212	-21.4679	-60.3979	-44.2188
23	1.7927	-0.2204	-0.2413	2.2903	0.4429	1.3944	-0.0532	-0.0624	0.1059	-0.0493	0.0444	0.2602	-0.0794	-0.3312	0.0148	0.0719	0.0093	0.0097	0.2166	0.0071	0.1554	-22.147	-41.7543	-50.8386
24	0.8394	-0.0418	0.2356	0.6518	-0.1559	1.069	-0.0214	-0.1047	-0.0008	0.0733	0.019	0.058	-0.0262	-0.1375	0.0082	0.0602	-0.007	0.0212	0.1169	-0.0083	0.0804	-5.8219	-44.6958	-46.2292
25	0.3345	0.072	0.1548	3.3168	2.1774	1.471	0.1437	-0.3565	-0.4158	0.2406	-0.1576	-0.0243	0.6698	-0.2729	0.0224	0.4284	-0.1569	-0.0399	0.3063	0.0929	0.3297	-5.4808	8.4193	-28.0382
26	2.8005	-2.1694	-1.9638	5.6845	2.2777	2.302	0.0995	-0.1297	-0.6181	0.6469	-0.2189	0.3814	0.3088	-0.3202	0.0407	0.4383	-0.2049	-0.0099	0.4179	0.0152	0.3905	-20.7602	6.6318	-41.68
27	1.3786	-0.1204	-0.108	1.9742	0.5973	1.6121	0.0154	0.0297	0.0073	0.0076	-0.1553	0.2383	-0.0111	-0.4639	-0.0171	0.093	-0.0207	0.004	0.2564	-0.0398	0.1537	-21.7883	24.0876	-48.528
28	1.045	-0.0916	0.2596	0.7795	0.0136	1.1954	0.0307	-0.0801	-0.0711	0.064	-0.0058	-0.0291	0.0559	-0.1347	-0.0381	0.0768	-0.0315	-0.0051	0.1017	-0.0054	0.1072	-5.1779	21.4429	-44.9953
29	4.1257	2.3928	-3.656	6.3564	-3.6339	5.1564	-0.0958	-0.0167	-0.54	-0.0367	-0.3139	-0.3311	0.7335	0.575	0.4082	0.3766	0.1485	0.0094	0.3255	-0.0802	0.2167	66.0903	-27.4711	-24.7844
30	7.6387	1.3537	-2.2872	4.1364	-0.5592	3.9181	-0.0462	0.0172	-1.0013	-0.3167	-0.1003	-0.4502	0.5716	0.2951	0.1701	0.3681	0.2187	-0.0132	0.4322	-0.0389	0.4398	79.6419	-31.1396	-10.0252
31	2.1041	0.1856	-0.5001	2.8122	-0.7095	1.5738	-0.0359	-0.028	0.0762	0.0662	-0.0682	-0.4314	-0.0036	0.4898	0.0848	0.1338	0.0325	-0.0021	0.3442	0.0121	0.2174	82.548	-11.7464	-5.7687
32	0.8321	-0.0656	0.2176	0.7762	-0.0174	1.1704	-0.0113	0.0507	-0.0248	-0.0167	0.026	-0.0884	0.0944	0.2189	-0.0112	0.1174	0.056	0.0089	0.2052	-0.0099	0.1084	65.8388	-13.2111	-9.0775

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 31:60 )	A	31 - 60
2	X-RAY DIFFRACTION	2	( chain A and resid 61:189 )	A	61 - 189
3	X-RAY DIFFRACTION	3	( chain A and resid 190:336 )	A	190 - 336
4	X-RAY DIFFRACTION	4	( chain A and resid 337:347 )	A	337 - 347
5	X-RAY DIFFRACTION	5	( chain B and resid 31:51 )	B	31 - 51
6	X-RAY DIFFRACTION	6	( chain B and resid 52:67 )	B	52 - 67
7	X-RAY DIFFRACTION	7	( chain B and resid 68:88 )	B	68 - 88
8	X-RAY DIFFRACTION	8	( chain B and resid 89:347 )	B	89 - 347
9	X-RAY DIFFRACTION	9	( chain C and resid 32:51 )	C	32 - 51
10	X-RAY DIFFRACTION	10	( chain C and resid 52:64 )	C	52 - 64
11	X-RAY DIFFRACTION	11	( chain C and resid 65:91 )	C	65 - 91
12	X-RAY DIFFRACTION	12	( chain C and resid 92:347 )	C	92 - 347
13	X-RAY DIFFRACTION	13	( chain D and resid 32:51 )	D	32 - 51
14	X-RAY DIFFRACTION	14	( chain D and resid 52:90 )	D	52 - 90
15	X-RAY DIFFRACTION	15	( chain D and resid 91:323 )	D	91 - 323
16	X-RAY DIFFRACTION	16	( chain D and resid 324:347 )	D	324 - 347
17	X-RAY DIFFRACTION	17	( chain E and resid 32:50 )	E	32 - 50
18	X-RAY DIFFRACTION	18	( chain E and resid 51:65 )	E	51 - 65
19	X-RAY DIFFRACTION	19	( chain E and resid 66:90 )	E	66 - 90
20	X-RAY DIFFRACTION	20	( chain E and resid 91:347 )	E	91 - 347
21	X-RAY DIFFRACTION	21	( chain F and resid 32:59 )	F	32 - 59
22	X-RAY DIFFRACTION	22	( chain F and resid 60:89 )	F	60 - 89
23	X-RAY DIFFRACTION	23	( chain F and resid 90:189 )	F	90 - 189
24	X-RAY DIFFRACTION	24	( chain F and resid 190:347 )	F	190 - 347
25	X-RAY DIFFRACTION	25	( chain G and resid 32:59 )	G	32 - 59
26	X-RAY DIFFRACTION	26	( chain G and resid 60:91 )	G	60 - 91
27	X-RAY DIFFRACTION	27	( chain G and resid 92:189 )	G	92 - 189
28	X-RAY DIFFRACTION	28	( chain G and resid 190:347 )	G	190 - 347
29	X-RAY DIFFRACTION	29	( chain H and resid 32:60 )	H	32 - 60
30	X-RAY DIFFRACTION	30	( chain H and resid 61:87 )	H	61 - 87
31	X-RAY DIFFRACTION	31	( chain H and resid 88:189 )	H	88 - 189
32	X-RAY DIFFRACTION	32	( chain H and resid 190:347 )	H	190 - 347

-
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