PDB-2z2o: Crystal Structure of apo virginiamycin B lyase from Staphylococcu...

ID or keywords:

Entry

Database: PDB / ID: 2z2o

Title

Crystal Structure of apo virginiamycin B lyase from Staphylococcus aureus

Components

virginiamycin B lyase

Keywords

LYASE / seven-bladed beta-propeller /

antibiotic resistance /

enzyme mechanism / virginiamycin B lyase / virginiamycin B hydrolase /

streptogramin

Function / homology

Function and homology information

carbon-oxygen lyase activity /

Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / antibiotic catabolic process / response to antibiotic / magnesium ion binding
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Korczynska, M. / Berghuis, A.M.

Citation

Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for streptogramin B resistance in Staphylococcus aureus by virginiamycin B lyase
Authors: Korczynska, M. / Mukhtar, T.A. / Wright, G.D. / Berghuis, A.M.

History

Deposition	May 25, 2007	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 19, 2007	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2007	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.3	Nov 1, 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	2z2o.cif.gz	264.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2z2o.ent.gz	214.4 KB	Display	PDB format
PDBx/mmJSON format	2z2o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z2/2z2o ftp://data.pdbj.org/pub/pdb/validation_reports/z2/2z2o	HTTPS FTP

-
Related structure data

Related structure data	2z2nSC 2z2pC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2qc5-d 4bh6-2 5z44-1 6iyy-d 6muj-2 4ggc-d 5z46-2 6lh7-2 5bu9-2 5ekx-1 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

2z2nSC

2z2pC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: virginiamycin B lyase

B: virginiamycin B lyase

C: virginiamycin B lyase

D: virginiamycin B lyase

hetero molecules

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

1

A: virginiamycin B lyase

hetero molecules

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

2

B: virginiamycin B lyase

hetero molecules

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

3

C: virginiamycin B lyase

hetero molecules

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

4

D: virginiamycin B lyase

hetero molecules

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

Unit cell

Length a, b, c (Å)	73.543, 79.231, 188.168
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	virginiamycin B lyase / Vgh protein / Hydrolase VgB Mass: 33082.285 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: BM30002, pIP524 / Gene: vgb, vgh / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q53744, UniProt: P17978*PLUS, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases, Isomerases; Intramolecular lyases
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1083 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THIS SEQUENCE DERIVES FROM THE ORIGINAL GENE.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.07 Å³/Da / Density % sol: 40.59 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50mM acetate buffer (pH 4.6), 25%(w/v) PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

Diffraction	Mean temperature: 95 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.0999 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0999 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. obs: 86401 / % possible obs: 98.9 % / Redundancy: 4.5 % / R_sym value: 0.081 / Net I/σ(I): 19.4
Reflection shell	Resolution: 1.9→1.97 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.5 / R_sym value: 0.461 / % possible all: 93.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2Z2N

2z2n

Resolution: 1.9→19.89 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.944 / SU B: 5.941 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The structure was refined also with CNS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19902	8108	9.3 %	RANDOM
R_work	0.14029	-	-	-
obs	0.14603	78962	99.74 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 21.662 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0 Å²	0 Å²
2-	-	-0.01 Å²	0 Å²
3-	-	-	0.01 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→19.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9210	0	5	1083	10298

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.022	9566
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	8512
X-RAY DIFFRACTION	r_angle_refined_deg	1.843	1.953	13041
X-RAY DIFFRACTION	r_angle_other_deg	0.963	3	20032
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.498	5	1234
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.371	25.625	416
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.234	15	1641
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.3	15	33
X-RAY DIFFRACTION	r_chiral_restr	0.13	0.2	1443
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	10692
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1785
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	1819
X-RAY DIFFRACTION	r_nbd_other	0.199	0.2	8805
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	4725
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	5648
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.205	0.2	860
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	0.247	0.2	57
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.245	0.2	148
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.242	0.2	59
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	1.227	1.5	6175
X-RAY DIFFRACTION	r_mcbond_other	0.358	1.5	2454
X-RAY DIFFRACTION	r_mcangle_it	1.841	2	9717
X-RAY DIFFRACTION	r_scbond_it	2.961	3	4010
X-RAY DIFFRACTION	r_scangle_it	4.29	4.5	3298
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.9→2.002 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.247	603	-
R_work	0.177	11705	-
obs	-	-	98.51 %

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	2.5576	-1.1582	-1.8803	6.812	4.1828	3.7309	-0.1116	-0.0703	-0.3103	1.0084	-0.2206	0.4773	0.6466	0.0924	0.3322	0.1576	-0.0454	0.0554	-0.1231	0.0385	-0.0345	-6.9657	-9.0263	-28.2911
2	1.239	-0.4442	-0.5922	1.7968	-0.1563	1.6404	-0.0511	-0.0706	-0.1131	0.0266	0.0106	0.2143	0.0595	-0.0787	0.0405	-0.0359	-0.0169	0.009	-0.0706	-0.0042	0.0198	-8.5289	-5.1829	-41.3417
3	1.6436	0.644	-0.8146	1.5508	-0.2359	1.2231	-0.0478	0.0628	-0.0206	-0.1613	0.0119	0.1315	0.0988	-0.086	0.0359	-0.0217	0.0005	-0.0186	-0.057	-0.0108	-0.014	-5.927	2.7186	-50.8484
4	1.0214	0.2567	0.119	1.1753	0.689	0.923	-0.0298	0.0299	0.0349	-0.0718	0.0173	0.0323	-0.0264	-0.0011	0.0125	-0.0238	0.003	-0.0004	-0.0669	0.0098	-0.0121	-1.0001	14.187	-49.636
5	1.0022	-0.0762	0.5833	1.0861	-0.183	1.3535	-0.0243	-0.041	0.0488	0.0178	0.0263	0.0359	-0.0958	-0.0047	-0.002	-0.0248	0.006	0.0124	-0.0643	-0.014	-0.0106	0.8015	20.193	-38.9957
6	1.044	-0.5219	0.3989	1.3522	-0.4505	1.2885	-0.0171	-0.0493	0.081	0.0807	-0.0019	-0.0345	-0.0704	0.0471	0.019	-0.0166	0.0239	0.0065	-0.0408	-0.022	-0.0374	0.3926	16.1412	-27.5245
7	2.68	-0.9258	0.2303	2.9482	1.0804	1.2333	-0.0943	-0.1569	-0.0872	0.2634	0.0511	0.0409	0.1933	-0.1225	0.0433	-0.005	0.0238	0.0348	-0.0368	0.019	-0.0568	-3.1025	5.4688	-22.8508
8	2.2071	-0.5379	-0.6262	5.9915	2.721	3.9206	-0.0258	-0.1714	0.0211	0.7131	-0.1346	0.1796	0.3887	-0.2251	0.1605	0.03	-0.0512	0.0757	-0.0335	-0.0104	-0.0541	-8.7979	-1.2141	-27.6132
9	11.3603	0.7324	-6.0344	3.2954	-0.8922	9.5077	-0.5115	-0.8845	-0.5564	0.4718	0.1009	-0.3691	0.7859	0.918	0.4106	0.063	0.1994	-0.0469	-0.0453	0.0822	-0.1871	-23.1305	15.6986	-1.3212
10	1.3381	0.2903	0.2948	0.9398	-0.4621	1.8693	-0.0296	-0.1485	-0.0406	-0.018	-0.0603	-0.0494	0.237	0.0928	0.0898	-0.0322	0.0384	0.0239	-0.0483	0.0133	-0.0275	-25.6416	16.3644	-15.177
11	0.68	0.1531	0.1006	1.7111	-0.3311	1.0312	0.0031	0.0527	-0.0748	-0.0501	-0.0233	-0.0388	0.1218	-0.0113	0.0202	-0.0236	-0.001	0.0091	-0.0319	0.0105	-0.0245	-30.4629	22.8251	-24.806
12	0.5242	-0.1397	-0.2245	1.4963	0.4248	1.1147	-0.0123	0.0336	0.0374	-0.0758	-0.01	0.0134	-0.02	-0.113	0.0223	-0.037	0.0042	-0.0106	-0.0277	0.0195	-0.0385	-37.571	33.1359	-24.0324
13	1.4367	-0.0582	0.1614	0.9631	0.4306	2.1102	-0.0127	0.0018	0.0528	0.0393	0.0146	0.0321	-0.0773	-0.1719	-0.0019	-0.0494	0.0295	-0.0006	-0.036	0.0186	-0.0265	-41.8887	38.2738	-13.7057
14	1.8833	-0.216	1.1357	1.4686	0.1217	2.3178	-0.0661	-0.0474	0.1698	0.1227	0.0718	-0.0278	-0.1412	-0.1813	-0.0057	-0.029	0.0228	0.0094	-0.0307	-0.0161	-0.0469	-39.2535	35.8277	-2.0323
15	2.1354	-0.8717	0.1513	1.5287	0.2733	2.0105	-0.1551	-0.2356	0.0123	0.1587	0.103	-0.0961	0.1073	0.0194	0.0521	-0.0163	0.02	-0.0088	0.0023	0.0007	-0.0777	-32.7803	26.9969	3.1226
16	5.9187	-0.6941	-2	1.5889	0.4239	3.2045	-0.1506	-0.2932	-0.1557	0.2915	0.1412	0.1179	0.3569	0.1386	0.0094	0.0196	0.0299	0.0109	-0.0333	0.0439	-0.0701	-30.2693	18.3515	-1.5537
17	11.1805	-8.3623	10.9601	10.4934	-9.2008	12.0223	0.3626	1.1626	-0.1939	-0.3168	-0.5101	0.0746	0.1937	1.0902	0.1475	-0.0393	0.07	0.0431	0.0545	-0.0952	-0.1794	8.1122	5.3225	-101.0405
18	2.3446	-0.8436	1.1925	3.1133	-1.7731	3.4506	0.0894	0.4413	-0.0229	-0.0685	-0.137	-0.0559	0.0187	0.4158	0.0477	-0.0809	0.0206	0.0108	0.0206	-0.0193	-0.0561	16.8668	6.1826	-89.612
19	2.3549	0.0978	-1.0616	1.1082	-0.8971	2.0092	0.0562	-0.0126	0.0039	-0.0122	-0.1126	-0.1199	-0.0489	0.2376	0.0564	-0.0523	0.0051	-0.0206	-0.039	0.0098	-0.0129	18.1342	7.2791	-77.1629
20	2.4265	0.6933	-0.9368	1.1771	-0.5347	1.9376	0.0831	-0.1066	-0.0148	-0.0148	-0.073	-0.0161	-0.0739	0.1242	-0.01	-0.0252	-0.0014	-0.0194	-0.0503	0.0021	-0.0383	8.704	8.9148	-69.0626
21	1.3745	0.1648	0.1918	1.0661	0.2514	1.7586	0.0808	-0.0052	-0.0132	0.0127	-0.0313	-0.0554	-0.1651	-0.2274	-0.0495	-0.033	0.0296	-0.0103	-0.0309	0.0073	-0.0392	-3.0754	11.2842	-71.8911
22	1.146	0.4372	0.0648	1.8727	0.1612	2.9578	0.1221	0.1058	-0.0175	-0.0123	-0.015	-0.0218	-0.1421	-0.5393	-0.1071	-0.0623	0.0682	-0.0485	0.0384	0.0007	-0.0538	-8.8359	10.5644	-82.6276
23	2.0576	-0.5586	-0.4434	3.0287	0.8084	3.837	0.0534	0.1503	-0.0418	-0.1789	-0.0096	0.1508	-0.1186	-0.4901	-0.0438	-0.0279	0.0568	-0.0542	0.0099	-0.0124	-0.0868	-4.5864	8.4398	-93.782
24	4.7321	-1.7151	1.3444	7.0739	-2.315	4.1184	0.2169	0.488	-0.0458	-0.3178	-0.1814	0.1863	-0.1716	0.0725	-0.0355	-0.0132	0.0485	-0.0147	-0.0042	-0.0219	-0.104	5.1257	9.7081	-96.7319
25	20.281	-4.4692	15.2715	1.6816	-3.3895	11.5002	-0.1495	-1.1371	-0.1502	0.2355	0.2415	0.1507	-0.0252	-0.8692	-0.092	-0.075	0.0785	0.0712	0.1562	0.0696	-0.1146	25.1332	-5.1387	-18.5367
26	3.3557	0.6663	1.4707	0.3461	-0.0412	3.2366	-0.1362	-0.3085	0.0621	0.0256	-0.0221	0.075	-0.1916	-0.124	0.1583	-0.0637	0.0716	-0.0184	-0.0015	-0.0448	-0.0393	20.888	2.9797	-30.0956
27	1.4054	-0.1235	0.2657	2.0815	1.5279	2.1187	-0.0732	-0.1093	0.1142	-0.0644	0.0229	0.0864	-0.1883	-0.1569	0.0503	-0.0392	0.0402	-0.0374	-0.0322	-0.0249	-0.0203	21.0225	5.0954	-42.547
28	1.101	-1.2477	-0.4194	1.8749	0.795	1.9089	0.0105	-0.0361	0.0645	-0.1531	-0.013	-0.0142	-0.1092	0.0101	0.0025	-0.0239	0.0045	-0.0139	-0.0491	-0.0131	-0.0358	27.5251	-1.6918	-50.8063
29	1.1033	-0.3924	-0.4689	1.055	-0.1069	1.6415	-0.0507	-0.0877	0.0251	0.0083	0.0846	0.026	0.1534	0.2979	-0.034	-0.0277	0.0489	-0.0192	-0.0101	-0.02	-0.0488	35.8777	-10.3463	-48.2196
30	1.0801	0.2901	-0.9051	1.912	-0.824	3.0754	-0.1295	-0.1432	-0.0207	0.0531	0.1492	0.0229	0.4738	0.5334	-0.0197	-0.0061	0.1518	-0.0173	0.0467	0.0226	-0.0821	38.542	-15.8888	-37.6829
31	3.1084	-0.1959	-0.8087	2.4156	-0.0978	2.4269	-0.205	-0.3756	-0.0971	0.225	0.2085	0.1324	0.3984	0.3933	-0.0035	-0.0049	0.1364	0.0116	0.0724	0.0447	-0.0977	34.9617	-13.8903	-26.3088
32	4.9284	-1.2536	2.8736	1.4356	-0.8344	3.3732	-0.1091	-0.4476	-0.1606	0.1136	0.1061	0.0645	-0.1704	-0.1931	0.003	-0.0565	0.0609	0.0053	0.0567	0.025	-0.0912	30.5038	-5.132	-23.2533

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 16
2	X-RAY DIFFRACTION	2	A	17 - 59
3	X-RAY DIFFRACTION	3	A	60 - 101
4	X-RAY DIFFRACTION	4	A	102 - 143
5	X-RAY DIFFRACTION	5	A	144 - 185
6	X-RAY DIFFRACTION	6	A	186 - 227
7	X-RAY DIFFRACTION	7	A	228 - 269
8	X-RAY DIFFRACTION	8	A	270 - 294
9	X-RAY DIFFRACTION	9	B	2 - 16
10	X-RAY DIFFRACTION	10	B	17 - 59
11	X-RAY DIFFRACTION	11	B	60 - 101
12	X-RAY DIFFRACTION	12	B	102 - 143
13	X-RAY DIFFRACTION	13	B	144 - 185
14	X-RAY DIFFRACTION	14	B	186 - 227
15	X-RAY DIFFRACTION	15	B	228 - 269
16	X-RAY DIFFRACTION	16	B	270 - 294
17	X-RAY DIFFRACTION	17	C	1 - 16
18	X-RAY DIFFRACTION	18	C	17 - 59
19	X-RAY DIFFRACTION	19	C	60 - 101
20	X-RAY DIFFRACTION	20	C	102 - 143
21	X-RAY DIFFRACTION	21	C	144 - 185
22	X-RAY DIFFRACTION	22	C	186 - 227
23	X-RAY DIFFRACTION	23	C	228 - 269
24	X-RAY DIFFRACTION	24	C	270 - 294
25	X-RAY DIFFRACTION	25	D	1 - 16
26	X-RAY DIFFRACTION	26	D	17 - 59
27	X-RAY DIFFRACTION	27	D	60 - 101
28	X-RAY DIFFRACTION	28	D	102 - 143
29	X-RAY DIFFRACTION	29	D	144 - 185
30	X-RAY DIFFRACTION	30	D	186 - 227
31	X-RAY DIFFRACTION	31	D	228 - 269
32	X-RAY DIFFRACTION	32	D	270 - 294

-
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