PDB-6mgy: Crystal Structure of the New Deli Metallo Beta Lactamase Variant ...

ID or keywords:

Entry

Database: PDB / ID: 6mgy

Title

Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 from Klebsiella pneumoniae

Components

Metallo-beta-lactamase NDM-5

Keywords

HYDROLASE / metallo beta lactamase / Carbapenemases /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

antibiotic catabolic process /

beta-lactamase activity /

beta-lactamase /

periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Kim, Y. / Tesar, C. / Jedrzejczak, R. / Babnigg, G. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 from Klebsiella pneumoniae
Authors: Kim, Y. / Tesar, C. / Jedrzejczak, R. / Babnigg, G. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Sep 16, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 3, 2018	Provider: repository / Type: Initial release
Revision 1.1	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6mgy.cif.gz	373.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6mgy.ent.gz	305.2 KB	Display	PDB format
PDBx/mmJSON format	6mgy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mg/6mgy ftp://data.pdbj.org/pub/pdb/validation_reports/mg/6mgy	HTTPS FTP

-
Related structure data

Similar structure data	6c89-2 5vbc-1 6xbf-4 6ogo-2 1bwq-d 3sfp-1 6xbe-1 6jv4-3 5ypi-6 2zaa-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) 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
Related items in Molecule of the Month	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (4) #105 - Sep 2008 Ribonuclease A similarity (2)

Deposited unit

A: Metallo-beta-lactamase NDM-5

B: Metallo-beta-lactamase NDM-5

C: Metallo-beta-lactamase NDM-5

D: Metallo-beta-lactamase NDM-5

hetero molecules

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

1

A: Metallo-beta-lactamase NDM-5

hetero molecules

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

2

B: Metallo-beta-lactamase NDM-5

hetero molecules

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

3

C: Metallo-beta-lactamase NDM-5

hetero molecules

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

4

D: Metallo-beta-lactamase NDM-5

hetero molecules

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

5

A: Metallo-beta-lactamase NDM-5

D: Metallo-beta-lactamase NDM-5

hetero molecules

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

6

B: Metallo-beta-lactamase NDM-5

C: Metallo-beta-lactamase NDM-5

hetero molecules

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

Unit cell

Length a, b, c (Å)	46.869, 69.619, 68.789
Angle α, β, γ (deg.)	92.26, 103.36, 88.52
Int Tables number	1
Space group name H-M	P1

#1: Protein	Metallo-beta-lactamase NDM-5 / NDM-5 / New Delhi Metallo carbapenemase protein Mass: 25713.904 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-5 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): gold / References: UniProt: U5TTL2, UniProt: C7C422*PLUS
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 640 / 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: 2.12 Å³/Da / Density % sol: 42.01 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M potassium thiocyante, 30 %(w/v) PEGMME 2000

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. obs: 102867 / % possible obs: 92.8 % / Redundancy: 2.1 % / B_iso Wilson estimate: 18.36 Å² / R_merge(I) obs: 0.056 / Net I/σ(I): 9.9
Reflection shell	Resolution: 1.6→1.63 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.334 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3263 / CC_1/2: 0.811 / % possible all: 58.5

-
Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→30.555 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / Phase error: 18.66

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1887	4911	4.77 %	random
R_work	0.1535	-	-	-
obs	0.1551	102855	92.56 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 25.2 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→30.555 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6865	0	16	640	7521

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	7217
X-RAY DIFFRACTION	f_angle_d	0.969	9852
X-RAY DIFFRACTION	f_dihedral_angle_d	16.149	2536
X-RAY DIFFRACTION	f_chiral_restr	0.064	1093
X-RAY DIFFRACTION	f_plane_restr	0.007	1318

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 (%)
1.6019-1.6201	0.2573	93	0.2262	1833	X-RAY DIFFRACTION	52
1.6201-1.6392	0.248	126	0.2161	2186	X-RAY DIFFRACTION	63
1.6392-1.6591	0.2709	151	0.2068	2401	X-RAY DIFFRACTION	69
1.6591-1.6801	0.232	135	0.1974	2759	X-RAY DIFFRACTION	78
1.6801-1.7022	0.2274	145	0.1979	3248	X-RAY DIFFRACTION	92
1.7022-1.7256	0.2248	171	0.1887	3375	X-RAY DIFFRACTION	95
1.7256-1.7502	0.239	148	0.1795	3339	X-RAY DIFFRACTION	95
1.7502-1.7763	0.226	178	0.1694	3374	X-RAY DIFFRACTION	96
1.7763-1.8041	0.2025	188	0.1617	3439	X-RAY DIFFRACTION	96
1.8041-1.8337	0.1868	156	0.1596	3353	X-RAY DIFFRACTION	96
1.8337-1.8653	0.2028	166	0.154	3412	X-RAY DIFFRACTION	96
1.8653-1.8992	0.1919	189	0.1519	3357	X-RAY DIFFRACTION	96
1.8992-1.9357	0.1944	183	0.1598	3421	X-RAY DIFFRACTION	97
1.9357-1.9752	0.1932	194	0.1572	3384	X-RAY DIFFRACTION	97
1.9752-2.0182	0.1988	184	0.152	3391	X-RAY DIFFRACTION	97
2.0182-2.0651	0.1855	181	0.1474	3384	X-RAY DIFFRACTION	97
2.0651-2.1167	0.1911	179	0.1478	3435	X-RAY DIFFRACTION	97
2.1167-2.1739	0.1721	152	0.1454	3482	X-RAY DIFFRACTION	97
2.1739-2.2379	0.1968	163	0.1484	3441	X-RAY DIFFRACTION	97
2.2379-2.3101	0.1847	158	0.1518	3410	X-RAY DIFFRACTION	97
2.3101-2.3926	0.1771	166	0.1556	3448	X-RAY DIFFRACTION	97
2.3926-2.4884	0.1959	160	0.1526	3463	X-RAY DIFFRACTION	98
2.4884-2.6016	0.1807	167	0.1577	3453	X-RAY DIFFRACTION	98
2.6016-2.7387	0.1964	172	0.159	3475	X-RAY DIFFRACTION	98
2.7387-2.9101	0.2003	164	0.1595	3459	X-RAY DIFFRACTION	98
2.9101-3.1346	0.193	176	0.1591	3479	X-RAY DIFFRACTION	98
3.1346-3.4497	0.1822	172	0.1519	3480	X-RAY DIFFRACTION	99
3.4497-3.948	0.1574	182	0.1414	3470	X-RAY DIFFRACTION	99
3.948-4.9705	0.1695	172	0.125	3451	X-RAY DIFFRACTION	98
4.9705-30.5601	0.1942	140	0.1591	3342	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	2.9342	-1.778	0.3359	5.9776	-0.4869	2.9954	0.0792	-0.1235	0.3674	0.3627	-0.1925	-0.5425	-0.1838	0.1842	0.093	0.2186	-0.0472	-0.0161	0.1697	-0.0096	0.1619	5.8932	3.8956	14.4871
2	6.7939	-0.3581	-1.7345	4.4444	-0.2566	3.8448	0.0377	0.084	-0.3562	-0.2179	-0.017	-0.6577	0.1996	0.8458	-0.1051	0.1568	0.0265	0.0198	0.2792	-0.0281	0.2002	11.9991	-0.4711	5.21
3	3.9777	0.064	0.2224	2.4284	0.3614	4.1111	0.1116	-0.2273	-0.0526	0.2031	-0.0975	-0.0316	0.1447	-0.0077	-0.021	0.1362	-0.0197	0.0166	0.1116	0.0019	0.1108	0.2121	-3.9766	10.2092
4	4.8259	1.2832	-2.5776	3.7695	-2.6741	8.3353	0.0432	0.0944	-0.2357	-0.1082	0.0608	-0.2397	0.6272	0.0832	-0.0844	0.22	0.0091	-0.0384	0.1255	-0.0319	0.1627	1.4859	-10.0235	1.2796
5	1.5276	-0.4255	0.6387	2.5696	0.0281	2.3437	0.0006	-0.0248	-0.0025	-0.0174	-0.021	0.1171	0.1094	-0.0649	0.0251	0.1279	-0.0191	0.0123	0.1133	-0.0038	0.121	-6.917	-4.6922	-6.5416
6	6.1974	2.2641	-2.1584	3.7304	-0.3788	5.8396	0.0223	-0.1663	0.1332	0.147	-0.0964	0.1451	-0.2967	-0.0368	0.0921	0.1868	0.0167	-0.0185	0.102	-0.0055	0.1584	-2.769	7.8589	-0.0729
7	1.9185	0.6022	0.2544	2.5661	0.8211	2.8424	-0.0848	0.1531	-0.035	-0.175	0.0921	-0.1046	-0.1307	0.2111	-0.04	0.1845	-0.0339	-0.007	0.1256	0.0237	0.1893	4.073	10.7743	-9.529
8	9.0957	-4.5744	0.2693	3.7994	0.272	2.4218	-0.22	-0.8659	0.6257	0.4831	0.2185	-0.372	-0.2229	0.2159	0.056	0.2594	-0.0034	-0.0155	0.2942	-0.0459	0.1621	23.5603	37.1692	11.2564
9	4.9415	0.3531	-0.2388	3.8033	-0.0632	3.0019	-0.0615	-0.0126	0.1992	0.0732	0.0879	-0.3884	-0.1911	0.4473	-0.0805	0.1366	-0.0356	-0.013	0.2085	-0.0059	0.1517	25.7684	37.1422	2.8842
10	4.7696	0.9952	-0.4273	2.1218	-0.6152	3.4311	0.1354	-0.2852	-0.1557	0.2107	-0.0622	-0.08	0.1392	0.1816	-0.0735	0.1797	-0.0207	-0.0187	0.1481	0.0168	0.1473	21.3504	27.3674	6.142
11	2.8372	1.1246	-0.6768	5.2053	-2.9507	5.1666	-0.0039	0.0154	-0.1342	-0.0317	0.0979	-0.264	0.2201	0.3361	-0.0864	0.1709	0.0257	-0.0286	0.1992	-0.021	0.1649	26.4749	26.9145	-4.8855
12	3.69	-2.1177	0.8507	2.224	-0.3402	2.4458	0.1093	0.1919	-0.1	-0.007	-0.0748	-0.0439	0.1292	0.1415	-0.0521	0.1276	-0.022	-0.0007	0.1005	0.0065	0.1166	18.3349	26.3823	-13.0454
13	0.8811	0.946	0.2815	2.8724	-0.9236	1.979	-0.0289	0.1401	-0.0676	0.0585	0.0468	-0.0193	0.0529	-0.1447	-0.0265	0.1251	0.0016	0.0164	0.099	-0.0073	0.1334	13.1703	32.036	-10.0985
14	4.0394	2.2709	-1.5312	6.3004	-1.2742	4.6717	0.0671	-0.1504	0.1083	0.3593	-0.0687	-0.0327	-0.2453	0.1115	-0.005	0.1767	0.0095	-0.0092	0.1279	-0.0111	0.1266	15.9848	43.027	-3.491
15	3.8954	0.7468	-0.5488	2.2894	-0.0898	2.7587	-0.0485	0.2803	0.2457	-0.0482	0.1581	-0.2945	-0.1544	0.2333	-0.082	0.1675	-0.0182	-0.0078	0.1162	-0.0117	0.1793	19.459	45.0109	-16.2056
16	1.2506	-0.6795	2.0986	4.8694	1.0697	4.56	-0.0558	-0.2331	0.2914	0.068	-0.1037	-0.2444	-0.3485	0.0553	0.1283	0.2286	-0.0143	0.0343	0.162	0.0256	0.1688	15.3557	45.0282	-1.5647
17	8.1148	1.6556	-4.5387	5.278	-2.5344	9.0947	0.0714	0.3192	0.3894	-0.3275	0.0428	-0.077	-0.3879	0.1212	-0.1581	0.2386	-0.0319	-0.0055	0.1432	0.0066	0.1947	17.7118	52.0243	-13.6021
18	3.0889	-1.0442	-1.2229	2.9281	0.2728	2.7752	-0.1657	0.1827	0.6957	-0.27	0.3111	-0.7198	-0.3901	0.4378	-0.0275	0.4164	-0.0294	0.0239	0.4307	-0.0102	0.3975	15.4845	35.9243	-55.9434
19	3.5832	0.6519	0.3135	4.3644	0.1548	3.5062	-0.0436	0.2702	0.1784	-0.0574	-0.0548	-0.3955	-0.1997	0.2264	0.0232	0.1042	-0.0185	0.0086	0.138	-0.0021	0.1315	14.5714	31.3363	-47.3675
20	3.1067	0.0348	1.2402	4.0438	-0.0992	3.9725	0.0006	0.0933	-0.0386	-0.1636	-0.0067	0.0666	-0.0262	-0.1998	0.0093	0.0699	-0.0098	0.0107	0.1165	-0.0141	0.09	4.8652	28.1341	-44.361
21	1.9887	-0.1748	0.6814	0.8978	0.1427	2.5326	-0.0163	-0.0716	-0.0194	0.0156	-0.0285	0.031	-0.0184	-0.133	0.0428	0.1142	-0.0033	0.0124	0.1311	-0.0202	0.142	10.6086	29.6847	-29.4077
22	6.837	3.8348	1.1437	6.5998	1.1602	4.5858	-0.0132	0.1875	-0.1558	-0.323	0.0034	0.0534	0.1494	0.1419	0.0212	0.1583	0.0517	0.0071	0.1633	-0.0137	0.1439	21.1811	24.5312	-38.472
23	2.5812	0.3029	0.639	1.4536	0.2273	3.6481	-0.0341	0.1552	0.0402	-0.0397	0.0277	-0.111	-0.1313	0.3495	-0.0058	0.1319	0.0144	0.0241	0.2178	-0.0037	0.2051	29.1576	30.5357	-34.7478
24	4.1091	-1.0244	0.3044	2.5084	-3.558	6.6338	0.242	0.6544	-0.0585	-0.5543	-0.2571	-0.3907	0.3931	0.4196	-0.1077	0.3224	0.0185	-0.0336	0.2742	-0.0266	0.147	-12.6019	-12.5584	-46.375
25	5.959	0.8791	-0.2016	6.2767	-0.2069	4.9496	0.0816	0.1522	0.5133	-0.3715	-0.0416	-0.3212	-0.1339	0.7189	-0.1234	0.2271	-0.0417	-0.0189	0.2421	0.0314	0.1795	-8.1831	-6.5162	-40.9229
26	2.7411	0.2765	1.4867	2.7057	-0.1709	4.7297	-0.0353	0.0098	0.064	-0.2397	0.043	0.0524	-0.0903	-0.1166	0.027	0.1736	-0.0218	-0.0233	0.1473	0.0326	0.1463	-17.3918	-4.4834	-36.1892
27	1.5405	-1.0517	1.1928	4.0986	-0.2766	2.6804	-0.1026	0.051	0.1378	0.0369	-0.0269	-0.0891	-0.1824	0.0347	0.094	0.1166	-0.0311	-0.0076	0.1208	0.0128	0.119	-12.5371	-3.4774	-20.9107
28	1.8311	-0.6126	0.4224	1.1187	0.4477	2.0113	0.0442	0.199	0.0118	-0.0827	0.0227	-0.0427	0.0487	0.3059	-0.0534	0.1956	0.0005	-0.0104	0.1685	0.0051	0.1617	-3.0662	-13.4122	-27.34
29	7.7491	3.662	1.3328	7.4136	2.0475	5.6484	0.2389	0.2054	-0.1453	0.2597	0.2154	-0.7165	-0.1574	0.9636	-0.4803	0.2532	0.0462	0.0124	0.3769	-0.0626	0.2398	9.4108	-15.4978	-27.2091

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 41 through 57 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 58 through 70 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 71 through 118 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 119 through 137 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 138 through 194 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 195 through 212 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 213 through 270 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 42 through 57 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 58 through 81 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 82 through 118 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 119 through 137 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 138 through 170 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 171 through 194 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 195 through 215 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 216 through 239 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 240 through 255 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 256 through 270 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 33 through 48 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 49 through 82 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 83 through 118 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 119 through 194 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 195 through 212 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 213 through 270 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 42 through 57 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 58 through 82 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 83 through 137 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 138 through 170 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 171 through 255 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 256 through 270 )

-
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