PDB-3tyx: Crystal structure of the F177S mutant of mycrocine immunity prote...

ID or keywords:

Entry

Database: PDB / ID: 3tyx

Title

Crystal structure of the F177S mutant of mycrocine immunity protein (MccF) with AMP

Components

Microcin immunity protein MccF

Keywords

IMMUNE SYSTEM / CSGID /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / MccF-like / AMP

Function / homology

Function and homology information

hydrolase activity /

nucleotide binding
Similarity search - Function

Biological species

Bacillus anthracis (anthrax bacterium)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.04 Å

Authors

Nocek, B. / Gu, M. / Zhou, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: J.Mol.Biol. / Year: 2012
Title: Structural and Functional Characterization of Microcin C Resistance Peptidase MccF from Bacillus anthracis.
Authors: Nocek, B. / Tikhonov, A. / Babnigg, G. / Gu, M. / Zhou, M. / Makarova, K.S. / Vondenhoff, G. / Aerschot, A.V. / Kwon, K. / Anderson, W.F. / Severinov, K. / Joachimiak, A.

History

Deposition	Sep 26, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 28, 2011	Provider: repository / Type: Initial release
Revision 1.1	May 2, 2012	Group: Database references
Revision 1.2	Jul 25, 2012	Group: Database references
Revision 1.3	Sep 13, 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_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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	3tyx.cif.gz	282.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3tyx.ent.gz	229.9 KB	Display	PDB format
PDBx/mmJSON format	3tyx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ty/3tyx ftp://data.pdbj.org/pub/pdb/validation_reports/ty/3tyx	HTTPS FTP

-
Related structure data

Related structure data	3gjzSC 3sr3C 3t5mC 3u1bC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4mi1-d 3u1b-d 3t5m-d 5k99-d 1hfb-3 4gyk-2 4iiy-d 3tlc-d 3tla-d 3tlg-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: IDP00038

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #57 - Sep 2004 Catalase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: Microcin immunity protein MccF

B: Microcin immunity protein MccF

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	118.230, 118.230, 54.839
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	78
Space group name H-M	P4₃

#1: Protein	Microcin immunity protein MccF Mass: 37963.199 Da / Num. of mol.: 2 / Mutation: F177S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BAS1809, BA_1949, GBAA_1949 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q81RT8, UniProt: A0A6L8PEJ7*PLUS
#2: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Comment: AMP*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.52 Å³/Da / Density % sol: 51.27 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M potassium chloride, 20% Peg 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2011 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.05→40 Å / Num. all: 48175 / Num. obs: 47231 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / B_iso Wilson estimate: 47 Å² / R_merge(I) obs: 0.083 / Net I/σ(I): 18
Reflection shell	Resolution: 2.05→2.09 Å / % possible all: 87.8

-
Processing

Software

Name	Version	Classification
SBC-Collect		data collection
MOLREP		phasing
REFMAC	5.6.0117	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3GJZ

3gjz

Resolution: 2.04→40 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.957 / SU B: 8.73 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2098	2389	5.1 %	RANDOM
R_work	0.16745	-	-	-
all	0.18	47208	-	-
obs	0.16863	44824	97.59 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 39.501 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.34 Å²	0 Å²	0 Å²
2-	-	-1.34 Å²	0 Å²
3-	-	-	2.68 Å²

Refinement step

Cycle: LAST / Resolution: 2.04→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5278	0	46	260	5584

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.02	5505
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3737
X-RAY DIFFRACTION	r_angle_refined_deg	1.882	1.976	7493
X-RAY DIFFRACTION	r_angle_other_deg	1.023	3	9148
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.554	5	677
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.885	24.568	243
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.051	15	923
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.845	15	23
X-RAY DIFFRACTION	r_chiral_restr	0.119	0.2	817
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	6080
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1105
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.043→2.096 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.301	136	-
R_work	0.245	2665	-
obs	-	-	81.42 %

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	4.7627	-6.7968	-6.3399	16.9475	17.0057	17.1814	0.4848	0.5287	0.4404	1.281	0.0688	-0.6694	1.5133	0.1554	-0.5536	0.591	0.2119	0.0637	0.1896	0.0585	0.3253	9.6849	45.5644	1.0517
2	1.6363	3.3517	0.4823	7.113	0.2889	2.7959	0.2581	0.0064	-0.8742	0.3496	-0.0012	-1.6156	0.518	-0.0163	-0.2569	0.1779	0.0347	-0.0339	0.1032	-0.1246	0.9173	-1.0703	30.6787	-13.1695
3	3.0745	1.0539	-1.0449	3.283	0.1535	0.4654	0.0586	0.3594	-0.5387	-0.5036	-0.1693	-0.5665	-0.0679	-0.1174	0.1107	0.244	0.1492	0.1418	0.2378	-0.0868	0.3041	3.1307	32.2258	-18.3629
4	0.8188	0.4505	-0.5486	1.385	0.5202	0.9845	-0.2481	-0.127	-0.4103	-0.0536	0.0276	-0.1902	0.2252	0.184	0.2205	0.0851	0.0695	0.1023	0.0924	0.0221	0.4384	-2.9666	24.2818	-4.7525
5	1.5695	-0.1157	-0.0186	0.0308	-0.0028	0.0119	0.0181	0.0071	-0.4794	-0.0585	-0.0135	-0.0143	0.016	0.024	-0.0046	0.1496	0.0339	0.1107	0.1235	0.0175	0.2961	-6.0613	32.2397	-4.1064
6	5.6059	4.3828	-4.2235	7.9637	-2.5951	3.3018	-0.1868	-0.3577	-0.2353	0.037	-0.0455	0.0223	0.1466	0.3253	0.2323	0.0501	0.0369	-0.0091	0.1904	0.1672	0.2597	3.4887	32.512	6.0096
7	1.0647	-0.1839	0.2246	0.3083	0.612	1.8491	-0.0222	-0.0545	-0.2493	-0.05	0.0112	-0.0373	-0.0237	0.0326	0.011	0.1268	0.0158	0.1055	0.1582	0.038	0.3203	-2.9398	39.717	-5.5328
8	2.6042	1.6171	1.0055	1.0205	0.5558	0.7014	-0.1901	0.2531	-0.0239	-0.1092	0.0871	-0.0566	-0.0986	0.2898	0.103	0.1282	-0.0055	0.1354	0.2431	0.0488	0.3057	2.7565	47.6628	-17.0669
9	1.3095	-0.0348	-1.4658	6.6641	-1.7139	2.1022	0.0917	-0.0412	0.3593	0.0145	0.1777	-0.4452	-0.0929	0.0073	-0.2694	0.0694	-0.0387	0.02	0.2012	-0.0323	0.2285	5.6715	57.0647	-6.5251
10	0.8173	-0.2492	-0.5921	0.5589	-0.3015	0.957	-0.0657	0.2761	-0.1767	0.0849	-0.1576	-0.0022	-0.0377	-0.0205	0.2233	0.1731	-0.0629	0.0621	0.3377	0.0027	0.1729	-10.4268	47.5351	-24.1524
11	0.8972	0.0901	-0.3847	1.2883	-0.7845	0.6079	-0.0435	-0.1194	-0.0519	0.0472	0.0038	-0.0834	-0.0453	0.0357	0.0397	0.1808	-0.0021	0.0357	0.1854	0.0188	0.1688	-12.292	48.861	0.8142
12	3.8405	3.9587	1.0163	12.5779	5.8093	2.9373	0.2891	-1.1082	-0.1887	0.7524	-0.2322	-0.196	0.3282	0.2189	-0.057	0.1174	-0.0243	-0.0052	0.4304	0.005	0.2576	-9.7322	50.327	10.3013
13	0.6614	0.3434	-0.0138	0.223	-0.1735	0.7046	-0.0061	0.019	-0.1211	-0.0048	0.0022	-0.0352	0.0175	0.0163	0.0039	0.1817	0.0089	0.0291	0.1694	0.0244	0.1806	-20.1978	47.3429	-0.7167
14	1.4202	0.5457	-0.4524	0.2177	-0.1353	0.4265	-0.0472	0.1227	0.0407	-0.0376	0.0665	0.0046	-0.0713	-0.0175	-0.0193	0.1846	0.0156	0.0321	0.1554	0.0273	0.1651	-18.4697	52.9492	-7.052
15	3.738	-2.3112	1.3522	3.754	-1.6403	0.7906	0.0841	-0.1229	0.0926	-0.0094	-0.1356	-0.0841	-0.0267	0.0972	0.0516	0.1554	-0.068	0.0334	0.2561	0.015	0.1519	-1.1439	56.3021	-2.3365
16	22.0347	-6.372	7.9351	1.8452	-2.2756	3.3243	-0.8243	-0.5664	1.2816	0.2492	0.1451	-0.3486	-0.7234	-0.5097	0.6792	0.7572	-0.0193	-0.0666	0.552	-0.2596	0.319	-48.5135	35.6927	19.7086
17	1.0214	0.3693	-0.4276	0.3393	-0.0829	0.5833	-0.0159	0.1803	-0.0533	-0.0153	-0.0599	0.0093	-0.1153	-0.1591	0.0759	0.1394	0.0053	0.0138	0.2015	-0.0294	0.2159	-50.5873	37.6097	-0.4682
18	5.1014	-1.0117	-4.0103	0.3462	1.199	4.2744	-0.0263	0.5527	0.5183	-0.0833	-0.1484	0.1125	-0.2366	-0.5497	0.1748	0.1299	0.0639	-0.0664	0.2568	0.084	0.439	-50.2771	46.2786	0.6993
19	1.664	0.6296	-0.6169	0.3507	-0.0867	0.9798	0.0332	0.0119	0.0962	0.0318	-0.0634	0.054	-0.0975	-0.0118	0.0302	0.1613	0.0103	0.0155	0.1725	0.0178	0.1611	-39.5811	47.4495	5.9302
20	1.4067	0.7675	0.0637	0.5886	0.5046	1.3848	-0.0521	-0.1079	-0.1273	-0.012	-0.101	0.0017	-0.025	-0.0084	0.1531	0.1567	-0.0156	0.0405	0.1885	0.0331	0.1984	-39.6249	36.4603	9.5026
21	1.1197	0.4599	0.8759	0.3329	-0.0113	2.1079	-0.2588	-0.0247	-0.4553	-0.1575	-0.0082	-0.2671	-0.0754	-0.0886	0.2669	0.1278	-0.0508	0.1471	0.1271	-0.0719	0.5871	-49.7922	23.8993	2.599
22	2.3173	-1.1597	1.4415	4.3215	0.2764	1.1664	0.0657	-0.2934	-0.4878	-0.1051	0.254	0.1116	0.011	-0.1305	-0.3197	0.1182	-0.0518	0.0596	0.2408	0.1079	0.2881	-50.0165	26.4637	15.8405
23	0.4488	0.4176	1.146	5.3354	7.2633	10.7363	0.1723	-0.1899	-0.3584	0.0766	-0.0969	0.2201	0.3568	-0.4582	-0.0754	0.1371	-0.1071	0.0428	0.1048	0.075	0.629	-42.6831	17.9421	11.3528
24	6.1873	-1.3868	-2.2768	1.3741	0.972	1.0389	0.1552	1.4425	-1.1039	-0.2835	-0.4665	-0.0341	-0.1586	-0.6052	0.3113	0.0688	0.0559	0.073	0.3973	-0.2931	0.4382	-42.9931	21.1467	-7.7373
25	1.2401	0.5439	-0.4719	1.1071	-0.2612	0.1884	-0.055	-0.2918	-0.3599	-0.028	-0.1022	-0.2275	-0.0016	0.11	0.1572	0.1566	-0.0042	0.0358	0.2008	0.1064	0.2656	-26.6354	29.3764	11.1374
26	2.397	-2.7208	1.27	11.2313	-10.9205	11.8659	0.2863	0.0217	0.0049	0.3759	-0.472	-0.129	-0.6543	0.7995	0.1858	0.1775	-0.0432	-0.0652	0.4124	0.0748	0.2224	-23.6	33.7231	18.4601
27	0.6832	-0.0636	-0.4969	0.3088	0.2592	0.5223	-0.1626	-0.0546	-0.5034	-0.0389	-0.091	-0.1121	0.0417	-0.0191	0.2536	0.1473	0.0094	0.1225	0.105	0.0886	0.4582	-23.6722	26.022	3.4231
28	2.5703	-0.6825	-1.676	0.7762	-0.0288	2.0671	-0.2407	-0.054	-0.6904	-0.0823	-0.1293	-0.2312	0.0943	-0.2741	0.37	0.0789	0.1185	0.2332	0.2708	0.3223	0.699	-19.0887	17.9503	5.315
29	2.7332	-0.5621	-0.0785	0.1168	0.0257	0.1227	-0.0913	-0.2167	-0.6706	0.0039	0.0406	0.1318	-0.1235	-0.0624	0.0507	0.2127	0.01	0.0528	0.1709	0.0613	0.3516	-36.7104	24.1095	9.0741
30	0.9535	-0.3924	-1.6284	3.9079	2.5915	3.7664	0.0792	-0.5767	-0.5603	-0.0581	-0.9339	-0.0004	-0.1261	0.3778	0.8547	0.0735	-0.0281	0.0403	0.7231	0.4145	0.4308	-37.5669	21.0217	18.693

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-1 - 8
2	X-RAY DIFFRACTION	2	A	9 - 27
3	X-RAY DIFFRACTION	3	A	28 - 51
4	X-RAY DIFFRACTION	4	A	52 - 77
5	X-RAY DIFFRACTION	5	A	78 - 94
6	X-RAY DIFFRACTION	6	A	95 - 105
7	X-RAY DIFFRACTION	7	A	106 - 142
8	X-RAY DIFFRACTION	8	A	143 - 159
9	X-RAY DIFFRACTION	9	A	160 - 167
10	X-RAY DIFFRACTION	10	A	168 - 193
11	X-RAY DIFFRACTION	11	A	194 - 223
12	X-RAY DIFFRACTION	12	A	224 - 229
13	X-RAY DIFFRACTION	13	A	230 - 257
14	X-RAY DIFFRACTION	14	A	258 - 309
15	X-RAY DIFFRACTION	15	A	310 - 333
16	X-RAY DIFFRACTION	16	B	2 - 8
17	X-RAY DIFFRACTION	17	B	9 - 42
18	X-RAY DIFFRACTION	18	B	43 - 52
19	X-RAY DIFFRACTION	19	B	53 - 103
20	X-RAY DIFFRACTION	20	B	104 - 141
21	X-RAY DIFFRACTION	21	B	142 - 154
22	X-RAY DIFFRACTION	22	B	155 - 160
23	X-RAY DIFFRACTION	23	B	161 - 173
24	X-RAY DIFFRACTION	24	B	174 - 194
25	X-RAY DIFFRACTION	25	B	195 - 222
26	X-RAY DIFFRACTION	26	B	223 - 228
27	X-RAY DIFFRACTION	27	B	229 - 277
28	X-RAY DIFFRACTION	28	B	278 - 295
29	X-RAY DIFFRACTION	29	B	296 - 317
30	X-RAY DIFFRACTION	30	B	318 - 333

-
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