PDB-5hw1: Crystal structure of TEM1 beta-lactamase in the presence of 1.2 M...

ID or keywords:

Entry

Database: PDB / ID: 5hw1

Title

Crystal structure of TEM1 beta-lactamase in the presence of 1.2 MPa xenon

Components

Beta-lactamase TEM

Keywords

HYDROLASE / xenon

Function / homology

Function and homology information

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

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Roose, B.W. / Dmochowski, I.J.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01-GM097478	United States
Department of Defense Lung Cancer Research Program	W81XWH-14-1-0424	United States

Citation

Journal: Chemphyschem / Year: 2018
Title: A Structural Basis for129Xe Hyper-CEST Signal in TEM-1 beta-Lactamase.
Authors: Roose, B.W. / Zemerov, S.D. / Wang, Y. / Kasimova, M.A. / Carnevale, V. / Dmochowski, I.J.

History

Deposition	Jan 28, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 28, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Jan 16, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5hw1.cif.gz	404.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5hw1.ent.gz	329.6 KB	Display	PDB format
PDBx/mmJSON format	5hw1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5hw1_validation.pdf.gz	435.5 KB	Display	wwPDB validaton report
Full document	5hw1_full_validation.pdf.gz	439.7 KB	Display
Data in XML	5hw1_validation.xml.gz	45 KB	Display
Data in CIF	5hw1_validation.cif.gz	65.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hw/5hw1 ftp://data.pdbj.org/pub/pdb/validation_reports/hw/5hw1	HTTPS FTP

-
Related structure data

Related structure data	5hviSC 5i52C 5i63C 5kkfC 5kpuC 6apaC 6aykC 5hw5 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5i63-1 5kkf-2 5hw5-4 5hvi-3 5kpu-4 5kkf-1 5iq8-4 4oqg-6 3jyi-6 6b2n-4 3jyi-3 5i52-1 5kpu-1 5i52-2 6ayk-2 1xpb-d 5kkf-3 1zg4-d 4ibx-1 1li0-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

Related structure data

5hviSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#164 - Aug 2013 Serotonin Receptor similarity (6) #222 - Jun 2018 Proteins and Nanoparticles similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (3) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (2)

Deposited unit

A: Beta-lactamase TEM

B: Beta-lactamase TEM

C: Beta-lactamase TEM

D: Beta-lactamase TEM

hetero molecules

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

1

A: Beta-lactamase TEM

hetero molecules

defined by author&software
29.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Beta-lactamase TEM

hetero molecules

defined by author&software
29.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Beta-lactamase TEM

hetero molecules

defined by author&software
29.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Beta-lactamase TEM

hetero molecules

defined by author&software
29.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	60.690, 84.610, 95.940
Angle α, β, γ (deg.)	90.000, 90.060, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Beta-lactamase TEM / IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 ...IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 / TEM-8/CAZ-2 Mass: 28911.904 Da / Num. of mol.: 4 / Mutation: M180T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6 / Plasmid: pJ411 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62593, beta-lactamase
#2: Chemical	ChemComp-XE / XENON Mass: 131.293 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Xe
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 812 / 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: 2.13 Å³/Da / Density % sol: 42.25 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 2% (v/v) tacsimate (pH 6.0), 0.1 M Bis-Tris (pH 6.5), 20% (w/v) PEG 3350 PH range: 6.0 - 7.0

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection twin	Operator: h,-k,-l / Fraction: 0.18
Reflection	Resolution: 1.7→51.27 Å / Num. obs: 106586 / % possible obs: 100 % / Redundancy: 7.1 % / CC_1/2: 0.998 / R_merge(I) obs: 0.097 / Net I/σ(I): 13.1
Reflection shell	Resolution: 1.7→1.73 Å / Redundancy: 7.1 % / R_merge(I) obs: 0.346 / Mean I/σ(I) obs: 5.6 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX		refinement
iMOSFLM		data reduction
Aimless	0.5.8	data scaling
PDB_EXTRACT	3.15	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5HVI

5hvi

Resolution: 1.7→51.265 Å / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 24.01

	R_factor	Num. reflection	% reflection
R_free	0.1904	10081	4.8 %
R_work	0.1515	-	-
obs	0.1533	106560	99.97 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 51.15 Å² / B_iso mean: 9.5305 Å² / B_iso min: 2.56 Å²

Refinement step

Cycle: final / Resolution: 1.7→51.265 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8023	0	11	812	8846
B_iso mean	-	-	14.41	18.15	-
Num. residues	-	-	-	-	1052

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	8180
X-RAY DIFFRACTION	f_angle_d	1.202	11098
X-RAY DIFFRACTION	f_chiral_restr	0.045	1290
X-RAY DIFFRACTION	f_plane_restr	0.006	1446
X-RAY DIFFRACTION	f_dihedral_angle_d	12.751	3040

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7001-1.7294	0.2107	502	0.1917	10051	10553	95
1.7294-1.7609	0.2171	458	0.186	9977	10435	96
1.7609-1.7947	0.1952	522	0.1816	10079	10601	95
1.7947-1.8314	0.2035	488	0.1776	9936	10424	95
1.8314-1.8712	0.1876	510	0.1718	9913	10423	95
1.8712-1.9147	0.1606	536	0.16	10014	10550	95
1.9147-1.9626	0.1953	490	0.1565	10077	10567	95
1.9626-2.0157	0.2016	550	0.1554	9908	10458	95
2.0157-2.075	0.1908	460	0.1571	10051	10511	96
2.075-2.142	0.1778	478	0.1511	10047	10525	95
2.142-2.2185	0.2114	467	0.1435	9961	10428	96
2.2185-2.3073	0.2048	518	0.1479	9955	10473	95
2.3073-2.4123	0.1844	474	0.1477	10121	10595	96
2.4123-2.5395	0.1909	556	0.1481	9900	10456	95
2.5395-2.6986	0.1985	548	0.1453	9915	10463	95
2.6986-2.907	0.1778	520	0.1446	10046	10566	95
2.907-3.1995	0.1802	500	0.1455	9965	10465	95
3.1995-3.6623	0.1846	474	0.1276	10019	10493	95
3.6623-4.6136	0.1763	506	0.1247	9970	10476	95
4.6136-49.336	0.1996	520	0.1732	9945	10465	95

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	2.1312	0.7542	0.4636	1.7153	-0.4229	1.0827	0.094	-0.185	-0.1753	0.0557	-0.0931	-0.0434	0.2734	-0.0254	0.0055	0.1339	0.0059	0.0313	0.0899	0.0207	0.0559	-7.0044	-24.1343	13.0403
2	0.5557	-0.043	0.0084	0.6308	0.3475	0.2166	-0.0323	0.0104	-0.1465	0.006	0.0059	0.037	0.3152	-0.197	0.0111	0.1645	-0.039	0.0181	0.0934	0.0021	0.056	-16.3329	-20.6872	9.5563
3	0.4601	0.0063	0.1757	0.0272	-0.0141	0.4474	-0.0256	0.0555	0.0307	-0.0196	0.0094	-0.0038	-0.0723	-0.0213	-0.0052	0.0847	-0.0044	0.0265	0.0342	-0.0037	0.0297	-18.4284	-8.2435	-13.6338
4	1.1266	-0.1752	0.3042	0.8977	-0.1317	0.9427	-0.0356	0.0804	0.0683	-0.0541	-0.0321	-0.0618	-0.0728	0.0495	0.024	0.0787	0.0068	0.0195	0.0338	-0.0017	0.0318	-6.9815	-5.8442	-15.8633
5	1.3803	0.3624	-0.5171	1.1241	-0.2043	1.589	0.0047	-0.0617	0.1211	0.0685	0.0402	0.1158	-0.0624	-0.1533	-0.0375	0.0649	0.0079	0.0086	0.0383	-0.0045	0.0319	-20.2471	-5.1196	-6.0284
6	0.6888	-0.1363	-0.0466	0.2564	0.0821	0.3914	0.0285	-0.1229	0.054	0.0958	0.0008	-0.0257	-0.1269	-0.0107	-0.0354	0.1061	-0.01	0.0195	0.0486	-0.0069	0.0274	-14.4305	-3.6878	4.7072
7	0.1632	-0.3926	-0.1538	0.9947	0.7233	2.593	0.0171	-0.0478	-0.049	-0.0278	-0.0505	0.0587	0.1528	-0.1991	0.0467	0.0826	-0.014	0.0122	0.0709	0.0103	0.0268	-20.0852	-18.6775	1.4815
8	1.4318	-0.2592	0.8648	0.888	0.0867	0.8111	-0.0126	-0.0713	-0.0904	0.0817	0.0115	0.0585	0.0726	-0.0646	0.1055	0.0864	-0.0031	0.0251	0.0282	-0.01	0.0276	-19.9111	-20.9838	-12.0084
9	0.707	-0.1622	-0.0415	0.6357	0.3234	0.7806	-0.0283	-0.0151	-0.0608	0.0308	-0.0085	-0.0388	0.0749	0.0453	-0.0225	0.0905	0.0022	0.0151	0.0279	-0.0059	0.0262	-6.5189	-21.5907	-0.4987
10	0.555	0.1046	-0.3248	2.0133	-0.7244	0.6471	-0.0574	-0.0905	-0.0211	-0.047	0.1025	-0.0724	0.2297	0.1407	-0.0132	0.1401	0.0291	0.0222	0.1066	-0.0169	0.0429	0.4799	-22.9314	6.3824
11	1.0775	-0.6695	0.0541	1.7182	0.2448	1.2901	0.0017	0.1749	-0.0695	-0.1546	-0.0235	0.0251	0.1312	-0.0919	0.0253	0.0871	-0.0192	0.0254	0.0992	-0.0097	0.0319	-38.9504	-24.1422	8.8178
12	0.6085	0.0132	-0.1549	1.4354	-0.2558	1.423	-0.0048	0.0972	-0.0731	-0.1218	0.0352	-0.0996	0.156	0.0795	0.0057	0.0742	-0.0013	0.0157	0.076	-0.0119	0.0411	-29.5565	-20.5186	12.288
13	0.4299	-0.0598	0.1529	0.1767	0.0935	0.147	-0.016	-0.0378	0.079	0.0454	0.0081	-0.0008	-0.03	-0.009	0.064	0.0828	0.0056	0.021	0.0136	-0.0018	0.0346	-27.2382	-8.2619	35.6092
14	0.3156	0.21	0.0735	0.4962	-0.2013	0.2672	-0.015	-0.0122	0.0526	0.0402	0.0122	0.0595	-0.0476	-0.0191	-0.0295	0.0756	-0.0081	0.0225	0.0101	0.0017	0.0328	-33.2164	-5.2385	33.767
15	0.857	-0.0397	-0.1317	0.5185	0.1637	0.0686	0.0249	0.1671	0.0858	-0.1738	-0.0018	0.0407	-0.1337	-0.0015	-0.0642	0.1387	-0.0019	0.0126	0.0571	0.0189	0.0461	-31.2533	-3.5578	17.3677
16	0.5295	0.1732	0.4622	0.6222	-0.5399	1.248	0.0405	0.0909	-0.0818	0.0252	-0.0092	-0.118	0.1064	0.1018	-0.0445	0.0641	0.005	-0.001	0.0414	-0.0181	0.039	-25.637	-18.6052	20.51
17	0.8375	-0.0449	0.2039	0.3996	-0.0441	0.49	-0.0081	0.0166	-0.0038	-0.0055	-0.0067	0.0104	-0.0045	-0.0398	-0.0061	0.0708	0	0.016	0.0086	0.0104	0.0237	-35.4326	-20.8939	27.5783
18	0.8853	0.2074	-0.1461	0.2867	0.0302	0.5119	-0.0255	0.0098	-0.1182	0.0003	0.0531	0.0154	0.0878	-0.0632	-0.0432	0.0884	-0.0068	0.0009	0.0311	0.0015	0.0332	-36.1743	-23.3878	19.186
19	1.7712	-1.6414	-0.4736	4.1558	0.5892	0.3039	0.0052	0.121	-0.0069	-0.087	0.0247	0.0458	0.0506	-0.0485	-0.0243	0.0824	-0.0037	0.0055	0.0516	-0.0019	0.0293	-46.6409	-22.455	15.8643
20	1.4434	0.2128	0.4791	2.1308	0.3714	0.9265	0.0687	-0.051	0.1247	0.0843	-0.1083	0.0788	-0.1409	-0.0754	0.0273	0.1013	0.0024	0.0055	0.0482	-0.0124	0.0372	-8.1004	-10.5098	61.0252
21	0.7585	-0.5479	0.0244	0.5444	-0.3274	0.6475	-0.0164	0.041	0.1362	0.0108	-0.0082	-0.1093	-0.1863	0.1622	-0.0024	0.1216	-0.024	0.0142	0.0649	0.004	0.0473	1.2999	-13.7054	57.4551
22	0.1331	-0.0268	-0.0227	0.163	0.0963	0.1244	-0.0086	0.0287	-0.0466	-0.031	0.002	-0.0091	0.0194	-0.0047	-0.0056	0.0834	-0.013	0.0106	0.0115	-0.0105	0.0318	3.1143	-26.1159	34.2336
23	0.456	0.2504	0.0028	1.2642	-0.0306	0.0011	-0.0427	0.0485	-0.0302	-0.0286	0.0076	0.0565	0.0543	-0.05	0.0191	0.0862	-0.0112	0.0143	0.0232	-0.0033	0.0382	-8.4191	-28.9295	32.0105
24	0.1817	0.0518	-0.0816	0.1519	0.1745	0.3441	0.0088	-0.0463	-0.0389	0.1159	0.0091	0.0006	0.087	0.0216	-0.0094	0.1102	-0.0053	0.0052	0.0198	-0.0043	0.0372	1.8043	-30.239	47.5288
25	0.2627	-0.0691	0.0047	0.0825	0.0449	0.0867	-0.0096	0.0036	0.044	-0.015	0.0044	-0.0083	-0.0442	-0.0029	-0.0338	0.1038	-0.018	0.0175	-0.0061	0.011	0.0315	-3.3605	-13.4991	45.2503
26	2.3187	2.54	0.2426	6.0795	0.2782	0.1642	-0.0023	-0.146	0.1451	0.0682	-0.0393	0.2802	-0.1603	-0.1828	0.049	0.1194	0.0253	0.0095	0.0955	-0.0029	0.0404	-15.695	-11.6281	54.2998
27	1.3243	0.3787	0.2661	1.0457	0.2281	0.1077	0.0359	-0.1248	0.1463	0.1097	-0.0667	0.0685	-0.1376	-0.0606	-0.0012	0.1306	-0.0016	0.0032	0.053	-0.0177	0.0505	-23.4032	31.8287	39.224
28	0.2953	-0.1719	0.2607	0.1289	-0.1419	0.2339	-0.0621	0.0237	0.1014	0.0141	0.0163	-0.0503	-0.1557	0.0484	-0.0078	0.1266	-0.015	0.0071	0.0419	-0.0062	0.0558	-13.6369	28.7699	35.4808
29	0.2003	-0.1538	-0.1404	0.4083	0.2309	0.2359	-0.0206	0.0329	-0.0286	-0.0517	-0.0029	-0.0119	0.0562	-0.0216	0.017	0.0897	-0.0122	-0.001	0.0145	-0.001	0.0297	-11.9881	16.3417	12.2884
30	0.396	0.1331	-0.3075	0.3084	-0.1034	0.2555	-0.082	0.1186	-0.07	-0.0506	0.0328	0.0616	0.2158	-0.2361	0.0077	0.1094	-0.0447	0.0108	0.0808	0.0004	0.0466	-23.5667	13.9766	9.8792
31	0.1612	0.0958	-0.1211	0.6785	0.4063	0.4601	-0.0232	-0.0023	-0.0341	0.0389	0.0394	-0.045	0.0717	0.0399	-0.085	0.0896	-0.0001	0.0217	0.0192	-0.0017	0.0307	-10.2447	12.9636	19.7658
32	0.0492	-0.027	0.02	0.116	0.0494	0.0452	0.0146	-0.0151	-0.0157	0.0634	0.005	-0.0013	0.03	0.0099	0.0179	0.1069	-0.0093	0.0166	0.0175	-0.0021	0.0261	-13.9735	16.8803	29.4432
33	0.4633	0.2503	0.0677	0.8794	0.0742	0.2646	0.0189	-0.0004	0.0398	0.0144	0.0135	-0.0859	-0.0559	0.0319	0.0116	0.0761	-0.0171	0.0211	0.0163	-0.0098	0.0387	-10.4173	29.0699	14.1932
34	0.4487	-0.0716	0.1212	0.4037	-0.2376	0.4717	-0.0032	0.0063	0.0255	-0.0092	-0.0234	0.011	-0.0285	-0.0312	-0.083	0.0878	-0.0041	0.0196	0.0152	0.0037	0.0181	-23.7689	29.696	25.6148
35	2.1163	1.7846	0.1524	6.0188	0.1003	0.9598	-0.066	-0.1042	0.1368	-0.0207	0.1087	0.2293	-0.0685	-0.2055	-0.0273	0.0906	0.0184	0.0148	0.0831	0.0108	0.0391	-30.9277	30.6828	32.3804

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 26 through 50 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 51 through 68 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 69 through 98 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 99 through 131 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 132 through 155 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 156 through 179 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 180 through 195 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 196 through 212 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 213 through 269 )	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 270 through 288 )	A
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 26 through 50 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 51 through 68 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 69 through 98 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 99 through 155 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 156 through 179 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 180 through 195 )	B
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 196 through 250 )	B
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 251 through 269 )	B
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 270 through 288 )	B
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 26 through 50 )	C
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 51 through 68 )	C
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 69 through 98 )	C
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 99 through 131 )	C
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 132 through 179 )	C
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 180 through 269 )	C
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 270 through 288 )	C
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 26 through 50 )	D
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 51 through 68 )	D
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 69 through 98 )	D
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 99 through 131 )	D
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 132 through 155 )	D
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 156 through 195 )	D
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 196 through 212 )	D
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 213 through 269 )	D
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 270 through 288 )	D

-
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

-
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