PDB-4mig: Pyranose 2-oxidase from Phanerochaete chrysosporium, recombinant ...

ID or keywords:

Entry

Database: PDB / ID: 4mig

Title

Pyranose 2-oxidase from Phanerochaete chrysosporium, recombinant wild type

Components

Pyranose 2-oxidase

Keywords

OXIDOREDUCTASE / HOMOTETRAMER / GMC OXIDOREDUCTASE / ROSSMANN FOLD / PHBH FOLD / PYRANOSE 2-OXIDASE / SUGAR OXIDOREDUCTASE / FLAVINYLATION / HYPHAE

Function / homology

Function and homology information

pyranose oxidase / pyranose oxidase activity / flavin adenine dinucleotide binding / periplasmic space
Similarity search - Function

Biological species

Phanerochaete chrysosporium (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Hassan, N. / Tan, T.C. / Spadiut, O. / Pisanelli, I. / Fusco, L. / Haltrich, D. / Peterbauer, C. / Divne, C.

Citation

Journal: FEBS Open Bio / Year: 2013
Title: Crystal structures of Phanerochaete chrysosporium pyranose 2-oxidase suggest that the N-terminus acts as a propeptide that assists in homotetramer assembly.
Authors: Hassan, N. / Tan, T.C. / Spadiut, O. / Pisanelli, I. / Fusco, L. / Haltrich, D. / Peterbauer, C.K. / Divne, C.

History

Deposition	Aug 31, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 11, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.2	Jul 29, 2020	Group: Data collection / Database references / Derived calculations Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.type / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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_type.id / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Oct 16, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4mig.cif.gz	925.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4mig.ent.gz	764.4 KB	Display	PDB format
PDBx/mmJSON format	4mig.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4mig_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	4mig_full_validation.pdf.gz	1.4 MB	Display
Data in XML	4mig_validation.xml.gz	113.4 KB	Display
Data in CIF	4mig_validation.cif.gz	155.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mi/4mig ftp://data.pdbj.org/pub/pdb/validation_reports/mi/4mig	HTTPS FTP

-
Related structure data

Related structure data	4mifC 4mihC C: citing same article (ref.)
Similar structure data	4mih-2 4mih-1 4mif-d 3glh-2 6ciq-1 2q2b-2 3q5e-d 4rxo-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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#77 - May 2006 Glucose Oxidase similarity (2)

Deposited unit

A: Pyranose 2-oxidase

B: Pyranose 2-oxidase

C: Pyranose 2-oxidase

D: Pyranose 2-oxidase

hetero molecules

293 kDa, 4 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)	89.544, 166.448, 91.844
Angle α, β, γ (deg.)	90.00, 106.41, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein

Pyranose 2-oxidase / P2O / P2Ox / POD / POx / PROD / Pyranose oxidase / FAD-oxidoreductase / Glucose 2-oxidase / ...

Mass: 72289.758 Da / Num. of mol.: 4 / Fragment: PYRANOSE 2-OXIDASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Phanerochaete chrysosporium (fungus) / Strain: K-3 / Gene: p2o, p2ox, pox / Plasmid: pET21a(+) / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6QWR1, pyranose oxidase

#2: Chemical

ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE

Mass: 787.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₅N₉O₁₅P₂

#3: Sugar

ChemComp-G3F / 3-deoxy-3-fluoro-beta-D-glucopyranose / 3-deoxy-3-fluoro-beta-D-glucose / 3-deoxy-3-fluoro-D-glucose / 3-deoxy-3-fluoro-glucose

Type: D-saccharide, beta linking / Mass: 182.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₁FO₅

#4: Chemical

ChemComp-MN / MANGANESE (II) ION

Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1644 / Source method: isolated from a natural source / Formula: H₂O

Has protein modification

Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.62 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M TRIS, 0.1 M MnCl2, 30% (w/v) PEG 400, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 23, 2009 / Details: mirrors
Radiation	Monochromator: double-crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→46.95 Å / Num. all: 235360 / Num. obs: 235360 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Net I/σ(I): 12.8
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.3 / % possible all: 98.6

-
Processing

Software

Name	Version	Classification
MAR345		data collection
PHASER		phasing
REFMAC	5.6.0117	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→44.05 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.936 / SU B: 5.249 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.114 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21427	1514	0.6 %	RANDOM
R_work	0.17334	-	-	-
obs	0.1736	233846	99.02 %	-
all	-	233846	-	-

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: 21.848 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.21 Å²	0 Å²	-0.9 Å²
2-	-	-0.43 Å²	0 Å²
3-	-	-	0.12 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→44.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18105	0	268	1644	20017

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.02	18992
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	12833
X-RAY DIFFRACTION	r_angle_refined_deg	2.003	1.965	25876
X-RAY DIFFRACTION	r_angle_other_deg	1.052	3	31233
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.878	5	2314
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.011	23.853	885
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.164	15	2986
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.88	15	122
X-RAY DIFFRACTION	r_chiral_restr	0.166	0.2	2837
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	20937
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3863

LS refinement shell

Resolution: 1.8→1.897 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.294	203	-
R_work	0.255	33592	-
obs	-	-	98.62 %

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	1.7532	0.0453	0.3356	1.1752	-0.4016	2.8965	0.0102	0.0798	-0.2159	-0.0837	-0.0513	-0.2556	0.293	0.2716	0.0411	0.0458	0.032	0.0115	0.0286	-0.0004	0.0813	117.4273	22.191	27.7706
2	0.3154	0.0062	0.3296	0.0614	-0.0084	0.5675	-0.0059	0.0025	-0.0319	-0.0434	0.0025	-0.0002	-0.0304	0.0005	0.0034	0.0599	-0.0002	0.0029	0.0523	0.0043	0.0465	106.7968	39.6142	16.895
3	1.0309	0.1604	-0.0814	1.4387	-0.7738	1.1538	-0.0485	0.03	0.0275	-0.0103	-0.0282	-0.1561	-0.0161	0.1111	0.0767	0.0053	-0.0053	-0.0047	0.0705	-0.0044	0.027	127.4491	42.8994	17.6336
4	0.5424	0.0522	-0.2225	0.5318	-0.2979	0.8725	-0.0206	-0.0185	-0.0427	0.0475	0.0077	0.0069	0.0493	-0.03	0.013	0.0435	0.007	-0.0174	0.0623	-0.0185	0.0371	106.3085	34.789	24.7954
5	1.5597	-0.4734	-1.2154	0.2939	0.1934	2.6049	-0.0639	0.1536	-0.0971	-0.076	-0.0614	-0.0241	0.1309	0.1308	0.1253	0.0695	-0.0148	0.023	0.0906	0.0189	0.0628	125.47	48.9371	6.0286
6	0.305	0.0301	-0.0366	0.3757	-0.2465	0.6253	-0.0179	-0.0116	0.0032	0.0159	-0.0085	0.0066	-0.0063	-0.03	0.0264	0.0333	0.0042	-0.0018	0.0439	-0.0103	0.0175	106.0643	45.0424	23.1022
7	2.1483	-0.5656	-0.0391	2.2066	0.0527	0.5897	0.0054	-0.309	-0.1584	0.2953	0.0056	0.0145	0.145	0.0914	-0.0109	0.0838	0.0174	-0.0219	0.0688	0.0071	0.0373	125.1395	7.7614	5.4865
8	0.2181	0.0152	-0.0097	0.6815	-0.0375	0.1726	0.0074	0.0183	-0.007	0.0329	-0.0214	-0.0769	-0.0112	0.0351	0.0139	0.0113	0.0109	-0.0032	0.0303	-0.0008	0.0376	116.2537	31.6488	-4.509
9	1.7637	-0.4586	-0.4211	0.8335	0.0387	1.1969	0.0359	0.0925	-0.1703	-0.1146	-0.0029	0.0379	0.1274	-0.0153	-0.033	0.117	-0.0106	-0.009	0.0089	-0.0234	0.1068	101.216	5.7883	-12.1647
10	0.9539	-0.1062	-0.0403	0.4167	-0.0994	0.4373	0.0097	-0.0134	-0.0652	0.0014	-0.0094	-0.1256	0.0751	0.1412	-0.0003	0.0801	0.0357	0.0082	0.0559	-0.0195	0.0975	119.6855	14.5629	-5.5271
11	2.0253	-0.5673	-1.625	1.2806	0.5806	2.6869	0.0271	-0.1608	0.1173	0.1226	0.0409	0.0307	-0.0928	0.0432	-0.068	0.088	0.0057	-0.0009	0.0592	-0.0014	0.1048	92.9064	19.8532	-5.1703
12	0.71	-0.0721	0.063	0.3992	-0.0727	0.3774	0.0158	0.057	-0.0527	-0.0438	-0.0025	-0.094	0.0593	0.11	-0.0133	0.0469	0.0265	0.0201	0.0441	-0.0161	0.0483	114.8851	17.1138	-16.5437
13	2.3573	0.2329	-0.7679	2.1645	-0.7362	1.0929	0.0135	0.2506	0.3018	-0.1474	0.0534	0.3534	-0.0981	-0.2144	-0.0669	0.0811	0.0065	-0.0569	0.0649	0.0171	0.1168	91.5891	83.1468	-34.0895
14	0.4409	-0.5653	-0.0727	1.391	0.0893	0.0537	0.0056	0.0224	0.0241	0.001	-0.0187	0.0167	-0.0023	0.0042	0.0131	0.0484	-0.0089	-0.0004	0.0486	0.0052	0.0117	99.5663	56.419	-23.5516
15	0.6674	-0.2093	-0.0603	0.6037	-0.0451	0.7342	-0.0376	-0.01	0.1038	0.0374	-0.0069	-0.065	-0.1047	0.0433	0.0445	0.0579	-0.0219	-0.0144	0.0114	0.0113	0.0625	103.7531	80.3327	-12.2011
16	0.49	-0.0557	-0.135	0.5052	-0.2059	1.0121	-0.0278	0.1324	0.0636	-0.1101	-0.0242	-0.0612	-0.0466	0.0498	0.052	0.059	-0.025	0.008	0.0492	0.0254	0.0671	105.6346	75.6098	-27.0972
17	2.701	0.7655	-0.8848	1.3774	-0.5435	1.0149	-0.0906	0.0886	-0.1348	-0.0117	0.0614	0.1254	0.0899	-0.1493	0.0292	0.1031	-0.005	-0.0019	0.0651	-0.007	0.0835	95.1089	70.5531	-1.4027
18	0.451	-0.0015	-0.0661	0.4724	-0.2004	0.6882	-0.0302	0.0875	0.0649	-0.0578	-0.0165	-0.0809	-0.0483	0.0993	0.0467	0.035	-0.0243	0.0071	0.0394	0.0211	0.0585	112.99	73.72	-18.6647
19	2.8338	-0.6333	0.8448	1.5087	0.1554	2.131	-0.0169	0.2935	0.3554	-0.19	-0.0182	-0.1422	-0.2602	0.1455	0.0351	0.0915	-0.0245	0.0048	0.0384	0.0404	0.0614	71.8468	68.1958	-34.7949
20	0.3778	0.0405	0.3266	0.1478	0.0083	0.5182	-0.006	0.0032	-0.0031	-0.0014	0.0089	-0.0436	-0.0371	0.0057	-0.0028	0.035	0.0066	0.0028	0.028	0.0006	0.0314	78.9146	51.0078	-21.8841
21	1.3994	-0.7296	-0.0659	1.5325	0.0217	1.0972	0.0453	0.1286	-0.0088	-0.1813	-0.0148	-0.0221	0.0894	0.102	-0.0305	0.057	-0.0117	0.0156	0.0976	-0.0099	0.0102	86.5014	44.5946	-41.6258
22	0.8366	-0.284	-0.101	0.4333	-0.0344	0.4564	-0.0205	0.0052	0.0591	-0.0026	0.0175	0.048	-0.0753	-0.0228	0.003	0.0895	-0.0179	-0.01	0.083	-0.0014	0.0615	71.286	56.7668	-24.9623
23	2.9911	0.3322	-0.9751	0.2021	-0.2693	0.8661	0.1249	-0.0199	0.2535	0.0119	-0.0331	-0.0314	-0.1012	0.167	-0.0918	0.0601	-0.0057	0.021	0.0886	-0.0163	0.0546	95.302	41.9058	-36.0544
24	0.6372	-0.2477	0.0865	0.3668	-0.0598	0.3072	-0.0123	-0.0205	0.0115	0.0051	0.0148	0.0224	-0.0157	-0.0141	-0.0026	0.0493	-0.009	0.0023	0.0536	0.0003	0.032	72.8824	45.3842	-23.0648

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	13 - 72
2	X-RAY DIFFRACTION	2	A	73 - 201
3	X-RAY DIFFRACTION	3	A	202 - 272
4	X-RAY DIFFRACTION	4	A	273 - 415
5	X-RAY DIFFRACTION	5	A	416 - 467
6	X-RAY DIFFRACTION	6	A	468 - 617
7	X-RAY DIFFRACTION	7	B	10 - 69
8	X-RAY DIFFRACTION	8	B	70 - 161
9	X-RAY DIFFRACTION	9	B	162 - 251
10	X-RAY DIFFRACTION	10	B	252 - 419
11	X-RAY DIFFRACTION	11	B	420 - 467
12	X-RAY DIFFRACTION	12	B	468 - 617
13	X-RAY DIFFRACTION	13	C	13 - 70
14	X-RAY DIFFRACTION	14	C	71 - 129
15	X-RAY DIFFRACTION	15	C	130 - 264
16	X-RAY DIFFRACTION	16	C	265 - 419
17	X-RAY DIFFRACTION	17	C	420 - 467
18	X-RAY DIFFRACTION	18	C	468 - 617
19	X-RAY DIFFRACTION	19	D	13 - 71
20	X-RAY DIFFRACTION	20	D	72 - 201
21	X-RAY DIFFRACTION	21	D	202 - 264
22	X-RAY DIFFRACTION	22	D	265 - 415
23	X-RAY DIFFRACTION	23	D	416 - 467
24	X-RAY DIFFRACTION	24	D	468 - 617

-
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