PDB-5zpn: Copper amine oxidase from Arthrobacter globiformis anaerobically ...

ID or keywords:

Entry

Database: PDB / ID: 5zpn

Title

Copper amine oxidase from Arthrobacter globiformis anaerobically reduced by phenylethylamine at pH 8 at 288 K (1)

Components

Phenylethylamine oxidase

Keywords

OXIDOREDUCTASE / COPPER AMINE OXIDASE / TOPAQUINONE / TPQ

Function / homology

Function and homology information

primary-amine oxidase / primary methylamine oxidase activity / amine metabolic process / quinone binding / copper ion binding
Similarity search - Function

Biological species

Arthrobacter globiformis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Murakawa, T. / Baba, S. / Kawano, Y. / Hayashi, H. / Yano, T. / Tanizawa, K. / Kumasaka, T. / Yamamoto, M. / Okajima, T.

Funding support

Japan, 6items

Organization	Grant number	Country
Japan Agency for Medical Research and Development (AMED)	0294	Japan
Japan Society for the Promotion of Science	17K07317	Japan
Japan Society for the Promotion of Science	JP26440037	Japan
Japan Society for the Promotion of Science	JP23770127	Japan
Japan Society for the Promotion of Science	JP15K05573	Japan
Japan Society for the Promotion of Science	JP16KT0055	Japan

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: In crystallothermodynamic analysis of conformational change of the topaquinone cofactor in bacterial copper amine oxidase.
Authors: Murakawa, T. / Baba, S. / Kawano, Y. / Hayashi, H. / Yano, T. / Kumasaka, T. / Yamamoto, M. / Tanizawa, K. / Okajima, T.

History

Deposition	Apr 16, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 19, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 23, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Nov 22, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn_type.id
Revision 1.3	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5zpn.cif.gz	532.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5zpn.ent.gz	434.2 KB	Display	PDB format
PDBx/mmJSON format	5zpn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5zpn_validation.pdf.gz	470.1 KB	Display	wwPDB validaton report
Full document	5zpn_full_validation.pdf.gz	479.3 KB	Display
Data in XML	5zpn_validation.xml.gz	55.9 KB	Display
Data in CIF	5zpn_validation.cif.gz	83.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zp/5zpn ftp://data.pdbj.org/pub/pdb/validation_reports/zp/5zpn	HTTPS FTP

-
Related structure data

Related structure data	5zouC 5zowC 5zoxC 5zoyC 5zozC 5zp0C 5zp1C 5zp2C 5zp3C 5zp4C 5zp5C 5zp6C 5zp7C 5zp8C 5zp9C 5zpaC 5zpbC 5zpcC 5zpdC 5zpeC 5zpfC 5zpgC 5zphC 5zpiC 5zpjC 5zpkC 5zplC 5zpmC 5zpoC 5zppC 5zpqC 5zprC 5zpsC 5zptC 1iu7S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5zoy-2 5zp2-2 5zp0-1 1iu7-d 1avk-1 5zpm-1 5zp4-1 5zou-d 5zpc-d 5zp3-1 1ui8-d 5zpq-2 5zoz-2 5zpp-2 5zp1-2 3x3x-2 2zl8-d 5zoz-1 5zpt-2 3x42-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phenylethylamine oxidase

B: Phenylethylamine oxidase

hetero molecules

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

1

A: Phenylethylamine oxidase

hetero molecules

A: Phenylethylamine oxidase

hetero molecules

defined by author&software
Evidence: native gel electrophoresis
138 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Phenylethylamine oxidase

hetero molecules

B: Phenylethylamine oxidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	192.715, 63.801, 158.805
Angle α, β, γ (deg.)	90.00, 116.99, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-1085- HOH
2	1	A-1139- HOH
3	1	A-1305- HOH
4	1	B-1074- HOH
5	1	B-1172- HOH
6	1	B-1283- HOH

-
Protein , 1 types, 2 molecules AB

#1: Protein	Phenylethylamine oxidase / Primary amine oxidase Mass: 68913.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Plasmid: pepo-2 / Production host: Escherichia coli (E. coli) / Strain (production host): CD03 / References: UniProt: P46881, primary-amine oxidase

-
Non-polymers , 5 types, 1039 molecules

#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-HY1 / PHENYLACETALDEHYDE Mass: 120.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₈O
#5: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1030 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.16 Å³/Da / Density % sol: 61.03 %
Crystal grow	Temperature: 289 K / Method: microdialysis / pH: 7.4 / Details: 1.05M potassium-sodium tartrate, 25mM HEPES

-
Data collection

Diffraction

Mean temperature: 288 K

Diffraction source

Source:

SYNCHROTRON / Site:

SPring-8

/ Beamline: BL38B1 / Wavelength: 1 Å

Detector

Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 8, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.6→50 Å / Num. obs: 226550 / % possible obs: 99.8 % / Redundancy: 3.7 % / B_iso Wilson estimate: 18.44 Å² / R_merge(I) obs: 0.072 / R_pim(I) all: 0.044 / R_rim(I) all: 0.085 / Χ²: 1.735 / Net I/σ(I): 8.5 / Num. measured all: 832216

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.6-1.63	3.5	0.748	11154	0.73	0.466	0.884	0.99	99.6
1.63-1.66	3.6	0.674	11275	0.793	0.415	0.793	1.019	99.9
1.66-1.69	3.7	0.569	11307	0.844	0.347	0.669	1.072	100
1.69-1.72	3.7	0.519	11315	0.858	0.314	0.608	1.097	100
1.72-1.76	3.7	0.443	11249	0.896	0.268	0.519	1.139	100
1.76-1.8	3.7	0.358	11288	0.93	0.216	0.419	1.199	99.9
1.8-1.85	3.7	0.308	11313	0.945	0.186	0.361	1.279	100
1.85-1.9	3.7	0.249	11272	0.963	0.15	0.291	1.379	99.9
1.9-1.95	3.7	0.204	11324	0.975	0.123	0.238	1.444	99.9
1.95-2.02	3.7	0.166	11283	0.981	0.1	0.194	1.6	99.9
2.02-2.09	3.7	0.146	11315	0.986	0.088	0.171	1.672	99.9
2.09-2.17	3.7	0.128	11287	0.988	0.077	0.149	1.739	99.8
2.17-2.27	3.7	0.113	11350	0.99	0.068	0.132	1.88	99.9
2.27-2.39	3.7	0.104	11301	0.992	0.063	0.122	2.071	99.9
2.39-2.54	3.7	0.102	11397	0.992	0.062	0.12	2.352	99.9
2.54-2.74	3.6	0.092	11319	0.993	0.056	0.108	2.651	99.9
2.74-3.01	3.6	0.079	11377	0.994	0.049	0.093	3.007	99.8
3.01-3.45	3.6	0.061	11387	0.996	0.038	0.072	3.065	99.8
3.45-4.34	3.6	0.037	11414	0.999	0.022	0.043	2.282	99.5
4.34-50	3.5	0.025	11623	0.999	0.016	0.03	1.853	99.2

-
Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.24	data extraction
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1iu7

1iu7

Resolution: 1.6→39.66 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.12 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.208	11156	4.93 %
R_work	0.184	-	-
obs	0.185	226217	99.6 %

Solvent computation

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

Displacement parameters

B_iso mean: 29.68 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→39.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9738	0	31	1030	10799

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	10383
X-RAY DIFFRACTION	f_angle_d	0.92	14216
X-RAY DIFFRACTION	f_dihedral_angle_d	16.759	6225
X-RAY DIFFRACTION	f_chiral_restr	0.06	1535
X-RAY DIFFRACTION	f_plane_restr	0.006	1898

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 (%)
1.5984-1.6165	0.3073	346	0.2915	6793	X-RAY DIFFRACTION	95
1.6165-1.6355	0.2918	427	0.2725	7147	X-RAY DIFFRACTION	100
1.6355-1.6555	0.2774	352	0.2624	7077	X-RAY DIFFRACTION	100
1.6555-1.6764	0.2666	377	0.2565	7203	X-RAY DIFFRACTION	100
1.6764-1.6985	0.2678	397	0.247	7077	X-RAY DIFFRACTION	100
1.6985-1.7218	0.2785	368	0.2464	7201	X-RAY DIFFRACTION	100
1.7218-1.7464	0.2744	365	0.2336	7130	X-RAY DIFFRACTION	100
1.7464-1.7724	0.2801	344	0.2312	7229	X-RAY DIFFRACTION	100
1.7724-1.8001	0.252	372	0.2262	7100	X-RAY DIFFRACTION	100
1.8001-1.8296	0.2566	377	0.2232	7134	X-RAY DIFFRACTION	100
1.8296-1.8612	0.2431	384	0.2135	7165	X-RAY DIFFRACTION	100
1.8612-1.895	0.2303	338	0.2017	7178	X-RAY DIFFRACTION	100
1.895-1.9315	0.2291	391	0.1979	7208	X-RAY DIFFRACTION	100
1.9315-1.9709	0.2225	329	0.1928	7156	X-RAY DIFFRACTION	100
1.9709-2.0138	0.2114	380	0.1864	7190	X-RAY DIFFRACTION	100
2.0138-2.0606	0.2244	405	0.1864	7173	X-RAY DIFFRACTION	100
2.0606-2.1121	0.2122	363	0.1909	7161	X-RAY DIFFRACTION	100
2.1121-2.1692	0.2204	376	0.1888	7158	X-RAY DIFFRACTION	100
2.1692-2.2331	0.2053	400	0.1856	7154	X-RAY DIFFRACTION	100
2.2331-2.3051	0.2292	380	0.186	7206	X-RAY DIFFRACTION	100
2.3051-2.3875	0.2174	342	0.183	7187	X-RAY DIFFRACTION	100
2.3875-2.4831	0.2179	390	0.1949	7210	X-RAY DIFFRACTION	100
2.4831-2.5961	0.2088	366	0.1934	7192	X-RAY DIFFRACTION	100
2.5961-2.7329	0.2257	375	0.1924	7186	X-RAY DIFFRACTION	100
2.7329-2.9041	0.1966	370	0.1924	7248	X-RAY DIFFRACTION	100
2.9041-3.1282	0.2068	352	0.1822	7219	X-RAY DIFFRACTION	100
3.1282-3.4429	0.1924	362	0.1632	7244	X-RAY DIFFRACTION	100
3.4429-3.9407	0.171	398	0.1468	7208	X-RAY DIFFRACTION	99
3.9407-4.9633	0.1476	350	0.1351	7285	X-RAY DIFFRACTION	99
4.9633-39.6699	0.1841	380	0.1664	7242	X-RAY DIFFRACTION	97

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	0.0453	-0.0034	-0.0393	0.6979	0.063	0.0375	0.1786	-0.2014	0.0778	0.4278	-0.278	0.1548	-0.1909	-0.0869	-0.077	0.3768	-0.1463	0.0794	0.5312	-0.1525	0.2126	175.988	32.476	36.298
2	1.705	1.147	-1.898	3.1403	0.3118	3.1785	0.1681	-0.1665	-0.0177	0.328	-0.3518	0.3996	-0.261	-0.3866	-0.0674	0.2136	-0.2359	0.1082	0.4396	-0.1348	0.2191	172.629	23.93	34.84
3	2.3083	0.4048	0.5153	0.2121	0.1539	0.1436	0.1071	-0.5404	0.0522	0.177	-0.1228	-0.0115	0.0502	0.06	-0.0096	0.2559	-0.23	-0.042	0.573	0.0597	0.2146	205.567	22.163	39.171
4	1.072	-0.1096	0.1858	0.2882	-0.1117	1.0454	0.0913	-0.2805	0.0404	0.0739	-0.1463	-0.0054	-0.1475	-0.0384	0.041	0.1901	-0.1228	0.0031	0.2935	-0.0114	0.1659	194.323	27.844	21.075
5	0.4825	0.067	0.0668	0.255	0.0046	0.9182	0.1232	-0.0784	-0.0306	0.0249	-0.165	0.0012	-0.036	-0.069	0.0314	0.144	-0.0378	-0.0011	0.3209	-0.0108	0.1697	187.2	22.455	8.266
6	0.9462	0.0046	0.1954	0.2431	0.0043	0.8573	0.1432	-0.1796	-0.0787	0.0516	-0.1737	0.0223	0.0371	-0.1303	0.021	0.1562	-0.0807	0.0003	0.3277	-0.0112	0.1766	184.4	16.396	12.789
7	1.3505	0.1108	-0.4575	1.3541	-0.7761	0.5608	-0.0215	0.2426	0.0723	-0.2727	0.0198	-0.0898	-0.1089	0.2131	0.0012	0.2497	-0.1375	0.0543	0.3262	0.0445	0.1839	174.353	0.867	34.903
8	2.2929	-0.3158	-1.5473	3.5804	-1.2687	1.6662	-0.0681	0.1802	-0.081	-0.2162	-0.0406	-0.4394	-0.1175	0.3765	-0.0069	0.1845	-0.0955	0.086	0.3573	0.0283	0.2116	177.557	-7.821	36.365
9	1.9469	-0.22	0.1932	0.3544	-0.1236	1.2999	-0.0227	0.632	-0.1029	-0.1711	0.0806	-0.0143	0.023	-0.011	-0.0601	0.1906	-0.0766	-0.013	0.3439	-0.0271	0.1598	145.541	-12.365	33.276
10	0.6455	-0.0886	0.1477	0.2581	0.0086	0.9755	-0.0529	0.1044	0.0224	-0.0263	0.0899	-0.0101	-0.0777	0.115	-0.0429	0.139	-0.0427	0.0016	0.0607	-0.0071	0.1553	163.131	-8.613	60.096
11	2.1295	0.2156	0.7224	0.1185	0.0472	0.7664	-0.0803	-0.0358	0.0854	0.0022	0.0761	0.0099	-0.0987	0.0048	0.0112	0.1376	-0.0167	0.0004	0.0636	0.005	0.1601	161.245	-7.146	66.526

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 9 THROUGH 44 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 45 THROUGH 95 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 96 THROUGH 138 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 139 THROUGH 277 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 278 THROUGH 516 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 517 THROUGH 628 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 9 THROUGH 44 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 45 THROUGH 95 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 96 THROUGH 191 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 192 THROUGH 581 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 582 THROUGH 628 )

-
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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 1039 molecules

-
Details

-
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

-Protein , 1 types, 2 molecules AB

-Non-polymers , 5 types, 1039 molecules

-Details

-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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 1039 molecules

-
Details

-
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