PDB-7oda: OXA-48-like Beta-lactamase OXA-436

ID or keywords:

Entry

Database: PDB / ID: 7oda

Title

OXA-48-like Beta-lactamase OXA-436

Components

Beta-lactamase

Keywords

HYDROLASE / beta-lactamase / antibiotic resistance

Function / homology

Function and homology information

penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function

Biological species

Enterobacter asburiae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.796 Å

Authors

Lund, B.A. / Thomassen, A.M. / Carlsen, T.J.W. / Leiros, H.K.S.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Biochemical and biophysical characterization of the OXA-48-like carbapenemase OXA-436.
Authors: Lund, B.A. / Thomassen, A.M. / Carlsen, T.J.W. / Leiros, H.K.S.

History

Deposition	Apr 29, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 8, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 13, 2021	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7oda.cif.gz	589.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7oda.ent.gz	493.4 KB	Display	PDB format
PDBx/mmJSON format	7oda.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7oda_validation.pdf.gz	466.6 KB	Display	wwPDB validaton report
Full document	7oda_full_validation.pdf.gz	473.9 KB	Display
Data in XML	7oda_validation.xml.gz	48.5 KB	Display
Data in CIF	7oda_validation.cif.gz	72.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/od/7oda ftp://data.pdbj.org/pub/pdb/validation_reports/od/7oda	HTTPS FTP

-
Related structure data

Related structure data	5dtkS S: Starting model for refinement
Similar structure data	5dtt-4 7oda-2 5dva-3 5dts-1 7aw5-d 6pxx-d 5dtt-2 5dtk-3 5oe2-2 6nlw-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

C: Beta-lactamase

D: Beta-lactamase

hetero molecules

113 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-lactamase

B: Beta-lactamase

hetero molecules

defined by author&software
Evidence: homology, Other homologs are known dimers
56.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Beta-lactamase

D: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	69.116, 94.571, 87.762
Angle α, β, γ (deg.)	90.000, 109.890, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Beta-lactamase Mass: 28190.918 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter asburiae (bacteria) / Gene: blaOXA-436 / Plasmid: pDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S2C593, beta-lactamase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1111 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.58 % / Description: plate-like
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.75 Details: 0.1 M HEPES pH 7.75, 0.2 M sodium acetate, 26.5% PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 18, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.796→44.261 Å / Num. obs: 94891 / % possible obs: 95.9 % / Redundancy: 3.4 % / B_iso Wilson estimate: 18.11 Å² / CC_1/2: 0.992 / R_rim(I) all: 0.147 / Net I/σ(I): 9.46
Reflection shell	Resolution: 1.796→1.86 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 9214 / CC_1/2: 0.586 / R_rim(I) all: 1.26 / % possible all: 93.4

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.89 Å	44.26 Å
Translation	2.89 Å	44.26 Å

-
Processing

Software

Name	Version	Classification
PHENIX	1.8.4_1496	refinement
PHASER	2.7.16	phasing
Aimless	0.5.23	data scaling
PDB_EXTRACT	3.22	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5dtk

5dtk

Resolution: 1.796→44.261 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.43 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2268	4637	4.89 %
R_work	0.1834	90113	-
obs	0.1855	94750	95.91 %

Solvent computation

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

Displacement parameters

B_iso max: 88.53 Å² / B_iso mean: 21.73 Å² / B_iso min: 7.93 Å²

Refinement step

Cycle: final / Resolution: 1.796→44.261 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7868	0	71	1111	9050
B_iso mean	-	-	24.62	31.29	-
Num. residues	-	-	-	-	956

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	8252
X-RAY DIFFRACTION	f_angle_d	1.099	11207
X-RAY DIFFRACTION	f_chiral_restr	0.05	1192
X-RAY DIFFRACTION	f_plane_restr	0.005	1448
X-RAY DIFFRACTION	f_dihedral_angle_d	11.959	2990

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 (%)
1.7965-1.8169	0.4447	147	0.4138	2761	X-RAY DIFFRACTION	88
1.8169-1.8383	0.3958	159	0.3973	2949	X-RAY DIFFRACTION	96
1.8383-1.8607	0.4242	167	0.3665	3016	X-RAY DIFFRACTION	96
1.8607-1.8843	0.377	137	0.3427	2998	X-RAY DIFFRACTION	96
1.8843-1.909	0.3094	165	0.3122	2968	X-RAY DIFFRACTION	96
1.909-1.9352	0.3833	164	0.3111	2939	X-RAY DIFFRACTION	95
1.9352-1.9628	0.3608	156	0.3155	2894	X-RAY DIFFRACTION	92
1.9628-1.9921	0.2675	159	0.2354	3022	X-RAY DIFFRACTION	96
1.9921-2.0233	0.2498	159	0.2067	3007	X-RAY DIFFRACTION	97
2.0233-2.0564	0.2178	160	0.1912	3009	X-RAY DIFFRACTION	97
2.0564-2.0919	0.272	182	0.2231	2941	X-RAY DIFFRACTION	95
2.0919-2.1299	0.2875	143	0.2418	2882	X-RAY DIFFRACTION	93
2.1299-2.1709	0.2393	172	0.1912	2996	X-RAY DIFFRACTION	97
2.1709-2.2152	0.2338	175	0.1805	3035	X-RAY DIFFRACTION	97
2.2152-2.2634	0.2335	146	0.1817	3037	X-RAY DIFFRACTION	96
2.2634-2.316	0.2929	113	0.211	2852	X-RAY DIFFRACTION	90
2.316-2.3739	0.1962	166	0.1671	3009	X-RAY DIFFRACTION	97
2.3739-2.4381	0.2019	157	0.1618	3079	X-RAY DIFFRACTION	98
2.4381-2.5099	0.1995	158	0.1623	3020	X-RAY DIFFRACTION	97
2.5099-2.5909	0.2063	151	0.1569	3087	X-RAY DIFFRACTION	98
2.5909-2.6835	0.224	137	0.1616	3082	X-RAY DIFFRACTION	98
2.6835-2.7909	0.2051	144	0.163	3012	X-RAY DIFFRACTION	96
2.7909-2.9179	0.1832	156	0.1609	3078	X-RAY DIFFRACTION	98
2.9179-3.0717	0.2252	167	0.1673	3079	X-RAY DIFFRACTION	98
3.0717-3.2641	0.1959	124	0.1697	3101	X-RAY DIFFRACTION	98
3.2641-3.516	0.2118	152	0.162	2999	X-RAY DIFFRACTION	96
3.516-3.8696	0.1766	144	0.1463	3052	X-RAY DIFFRACTION	96
3.8696-4.4291	0.1902	153	0.1373	2974	X-RAY DIFFRACTION	94
4.4291-5.5785	0.1594	112	0.1315	3116	X-RAY DIFFRACTION	97
5.5785-44.261	0.1952	212	0.1603	3119	X-RAY DIFFRACTION	98

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	0.1354	0.017	0.0023	0.0888	0.0086	0.0106	-0.0993	-0.1179	-0.4057	0.0499	0.2419	-0.0889	0.0333	-0.0751	0.0045	0.2768	-0.0337	-0.0065	0.2361	0.1093	0.3618	-30.847	-24.079	13.257
2	0.1281	-0.0055	0.1412	0.2102	0.1097	0.3862	-0.0305	0.0452	-0.1833	0.0125	-0.0138	0.1858	0.0297	-0.2029	-0.0763	0.1023	-0.0141	0.0175	0.1276	0.0174	0.2507	-30.255	-15.397	0.823
3	0.0441	0.0294	0.0156	0.0617	-0.0365	0.0575	0.1104	-0.0203	0.2207	0.0338	0.0741	0.0697	-0.0282	-0.0977	0.0006	0.1821	0.045	0.0396	0.1681	-0.0075	0.2079	-22.949	10.243	-4.017
4	0.0316	-0.0074	-0.0384	0.0067	0.0084	0.0457	0.1113	-0.0354	0.1576	0.059	-0.0279	0.0647	-0.0307	-0.0432	0.0097	0.1768	0.0222	0.0247	0.1533	-0.0242	0.1535	-21.018	5.851	2.173
5	0.1291	0.0238	-0.0953	0.0393	-0.0315	0.1783	0.0481	0.13	0.1481	0.0136	0.0179	0.0499	-0.1113	-0.2099	0.0386	0.1201	0.0441	-0.0259	0.2048	0.0477	0.1756	-32.904	0.45	-11.329
6	0.1282	-0.0905	0.0268	0.0715	-0.0859	0.2915	0.0512	0.1573	-0.0687	-0.0798	-0.068	0.1261	-0.0207	-0.1178	-0.0179	0.1331	0.0166	-0.0291	0.1608	-0.0092	0.1711	-29.59	-8.768	-7.756
7	0.0904	0.0754	0.0466	0.1193	-0.0441	0.1322	-0.0354	-0.0131	-0.0104	0.0312	-0.0025	0.1154	0.0732	-0.0354	-0.0085	0.1037	0.0006	-0.0012	0.1392	0.0065	0.1553	-22.55	-10.948	4.112
8	0.0409	0.024	0.0251	0.0205	-0.0061	0.0714	-0.0427	-0.247	-0.1314	0.0895	0.0158	0.1984	-0.0885	-0.0326	0.0001	0.1752	0.0035	0.0262	0.2179	0.0168	0.1553	-24.409	-15.415	10.931
9	0.1378	-0.0009	-0.035	0	0.0006	0.0097	0.0516	-0.2083	0.1004	0.1734	-0.0393	-0.0879	0.0733	-0.0338	0.294	0.3473	-0.0262	-0.1912	0.4098	-0.1373	0.2761	13.293	3.902	10.124
10	0.2888	-0.1463	-0.1675	0.2656	-0.0204	0.1352	0.0096	-0.0677	0.043	-0.0013	0.0282	-0.2673	0.0417	0.0752	-0.0665	0.1124	-0.0017	-0.028	0.0962	-0.029	0.1812	9.004	-0.809	-3.85
11	0.076	0.072	-0.0125	0.0674	0.0085	0.1076	0.1193	-0.1142	-0.0445	-0.1558	0.0241	-0.026	0.2598	0.033	0.0214	0.2287	0.03	-0.0144	0.1141	0.032	0.151	-0.555	-24.448	-12.45
12	0.317	-0.022	-0.0722	0.0948	0.0488	0.0381	0.1011	-0.1154	0.058	-0.0851	-0.1081	-0.0325	0.1871	-0.0081	0.0093	0.1497	-0.0006	-0.017	0.0946	0.0402	0.1185	-0.169	-21.856	-5.109
13	0.063	-0.0091	0.0433	0.0284	-0.0057	0.0455	0.0021	-0.0155	-0.0243	-0.0401	0.0234	-0.0409	-0.0009	0.089	0.0058	0.1605	0.0033	0.0234	0.1112	-0.008	0.1265	6.937	-13.885	-19.447
14	0.2387	-0.0879	0.0433	0.6629	0.0548	0.1629	0.0224	-0.056	0.0379	0.0307	0.002	-0.1556	-0.0203	0.0107	-0.0042	0.1123	0.0053	-0.0097	0.1004	-0.004	0.1173	4.883	-5.233	-6.196
15	0.7306	0.3731	-0.0384	0.7376	0.0184	0.4764	0.0552	-0.2443	-0.0778	0.2123	0.0024	-0.153	0.0515	0.0815	-0.1303	0.2911	0.0328	-0.0883	0.2891	-0.032	0.103	5.077	-3.65	10.184
16	0.5954	0.008	0.3291	0.0441	0.0904	0.3536	0.0867	0.1168	-0.2591	-0.111	0.0283	-0.0263	-0.0374	0.033	0.5499	0.2768	0.0289	0.1686	0.1884	-0.0875	0.4147	0.212	-8.421	36.394
17	0.2934	0.2506	-0.1559	0.2189	-0.1111	0.2036	-0.0719	-0.0065	-0.1381	0.0329	0.0199	-0.2001	0.017	0.0819	-0.0891	0.1177	0.0027	0.0024	0.1129	0.0102	0.2137	-4.493	3.141	46.596
18	0.0645	0.0722	-0.0297	0.1025	0.0242	0.1333	0.0537	0.0486	0.0408	-0.051	0.0466	0.0843	-0.0274	0.0063	0.0447	0.1425	-0.0124	0.0127	0.1196	0.0411	0.1374	-13.814	24.377	38.799
19	0.1655	0.0198	-0.0224	0.0178	0.0377	0.1053	0.1178	-0.0942	0.1105	0.1218	0.0161	0.0022	-0.1319	0.0383	0.0394	0.1823	-0.0405	-0.0053	0.1555	-0.0063	0.1391	-6.534	22.176	53.313
20	0.3276	0.1374	-0.1575	0.5797	-0.0011	0.0869	-0.0073	0.0173	-0.1416	0.0084	0.0001	-0.1004	-0.0088	0.0162	0.0001	0.1125	-0.0104	-0.003	0.1069	0.0071	0.1209	-8.46	7.613	46.248
21	0.0253	-0.0238	-0.0004	0.0609	0.0445	0.0483	0.0433	0.1883	-0.1046	-0.1454	-0.0757	-0.0274	-0.0502	-0.051	0.0049	0.2051	-0.028	0.0302	0.2007	-0.0558	0.1796	-8.143	-1.96	32.765
22	0.0341	0.0026	-0.0107	0.0228	0.0158	0.0359	-0.056	0.2912	0.1656	-0.0699	0.021	-0.0057	-0.0126	-0.0999	0.0001	0.2671	-0.0281	-0.0207	0.4711	0.0305	0.1946	-42.738	13.045	19.08
23	0.186	0.0216	0.0944	0.0887	0.0396	0.1389	-0.0267	0.2721	0.1222	-0.0378	0.0113	-0.0628	-0.1322	-0.1117	-0.0055	0.1835	-0.0011	-0.0343	0.2594	0.0613	0.1723	-41.026	17.349	27.031
24	0.1759	0.0254	-0.0549	0.1333	-0.0544	0.0322	-0.0259	0.1024	0.0443	0.0232	0.0911	0.1018	-0.0609	-0.1449	-0.0025	0.1119	0.0129	0.008	0.1504	0.0415	0.1142	-45.371	8.088	41.416
25	0.1842	-0.1761	0.0275	0.1669	-0.0439	0.1213	0.0161	0.083	-0.1206	0.0474	-0.0048	0.0674	-0.0182	-0.0791	0.0003	0.1423	-0.0087	-0.0046	0.1227	0.0015	0.1687	-35.195	-6.884	48.263
26	0.1085	-0.0213	0.0409	0.0712	-0.0018	0.1098	0.0353	-0.0888	-0.0351	0.0199	-0.0035	-0.0253	0.0989	-0.1728	0.0124	0.1211	-0.0019	-0.0013	0.1756	0.0188	0.1244	-46.46	3.477	53.214
27	0.1761	0.0208	-0.0619	0.0096	0.049	0.3274	0.0469	-0.0311	0.0545	0.0607	-0.0082	0.0321	-0.0301	-0.0942	0	0.1132	0.0015	0.0015	0.1355	0.0282	0.118	-43.075	11.302	45.341
28	0.1218	-0.0895	-0.1205	0.0832	0.1323	0.216	-0.1048	0.1773	0.0091	-0.0893	0.0685	0.0609	0.0465	-0.0948	-0.0154	0.1131	-0.0222	-0.0048	0.1837	0.0038	0.1114	-35.753	6.973	34.091
29	0.0554	-0.0558	0.0264	0.0588	-0.0427	0.0787	0.0591	0.2894	-0.0066	0.0473	-0.0451	-0.0124	0.0783	-0.0542	-0.0166	0.1533	-0.021	-0.0064	0.2139	0.0201	0.1241	-40.723	8.712	29.627
30	0.0623	-0.0444	0.0421	0.0498	0.0016	0.0817	0.021	0.2396	0.0715	0.0708	-0.037	0.0398	0.1028	0.1585	-0.0255	0.1706	-0.022	0.0028	0.3383	-0.0127	0.1211	-34.916	6.715	23.904

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 25:38 )	A	25 - 38
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 39:82 )	A	39 - 82
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 83:102 )	A	83 - 102
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 103:119 )	A	103 - 119
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 120:142 )	A	120 - 142
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 143:194 )	A	143 - 194
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 195:231 )	A	195 - 231
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 232:265 )	A	232 - 265
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 25:38 )	B	25 - 38
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 39:82 )	B	39 - 82
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 83:102 )	B	83 - 102
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 103:119 )	B	103 - 119
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 120:142 )	B	120 - 142
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 143:243 )	B	143 - 243
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 244:265 )	B	244 - 265
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 25:38 )	C	25 - 38
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 39:83 )	C	39 - 83
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 84:119 )	C	84 - 119
19	X-RAY DIFFRACTION	19	( CHAIN C AND RESID 120:141 )	C	120 - 141
20	X-RAY DIFFRACTION	20	( CHAIN C AND RESID 142:243 )	C	142 - 243
21	X-RAY DIFFRACTION	21	( CHAIN C AND RESID 244:265 )	C	244 - 265
22	X-RAY DIFFRACTION	22	( CHAIN D AND RESID 25:38 )	D	25 - 38
23	X-RAY DIFFRACTION	23	( CHAIN D AND RESID 39:58 )	D	39 - 58
24	X-RAY DIFFRACTION	24	( CHAIN D AND RESID 59:83 )	D	59 - 83
25	X-RAY DIFFRACTION	25	( CHAIN D AND RESID 84:119 )	D	84 - 119
26	X-RAY DIFFRACTION	26	( CHAIN D AND RESID 120:141 )	D	120 - 141
27	X-RAY DIFFRACTION	27	( CHAIN D AND RESID 142:194 )	D	142 - 194
28	X-RAY DIFFRACTION	28	( CHAIN D AND RESID 195:231 )	D	195 - 231
29	X-RAY DIFFRACTION	29	( CHAIN D AND RESID 232:243 )	D	232 - 243
30	X-RAY DIFFRACTION	30	( CHAIN D AND RESID 244:265 )	D	244 - 265

-
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

-
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