PDB-5c0u: Crystal structure of the copper-bound form of MerB mutant D99S

ID or keywords:

Entry

Database: PDB / ID: 5c0u

Title

Crystal structure of the copper-bound form of MerB mutant D99S

Components

Alkylmercury lyase

Keywords

LYASE / METAL BINDING PROTEIN /

Bacterial Proteins /

Cysteine /

Escherichia coli /

Lyases /

copper /

Mutation

Function / homology

Function and homology information

alkylmercury lyase /

alkylmercury lyase activity /

: / response to mercury ion
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.87 Å

Authors

Wahba, H.M. / Lecoq, L. / Stevenson, M. / Mansour, A. / Cappadocia, L. / Lafrance-Vanasse, J. / Wilkinson, K.J. / Sygusch, J. / Wilcox, D.E. / Omichinski, J.G.

Funding support

Canada,

United States, 2items

Citation

Journal: Biochemistry / Year: 2016
Title: Structural and Biochemical Characterization of a Copper-Binding Mutant of the Organomercurial Lyase MerB: Insight into the Key Role of the Active Site Aspartic Acid in Hg-Carbon Bond Cleavage ...
Authors: Wahba, H.M. / Lecoq, L. / Stevenson, M. / Mansour, A. / Cappadocia, L. / Lafrance-Vanasse, J. / Wilkinson, K.J. / Sygusch, J. / Wilcox, D.E. / Omichinski, J.G.

History

Deposition	Jun 12, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 3, 2016	Provider: repository / Type: Initial release
Revision 1.1	Feb 10, 2016	Group: Database references
Revision 1.2	Feb 24, 2016	Group: Database references
Revision 1.3	Mar 2, 2016	Group: Database references
Revision 1.4	Sep 27, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5c0u.cif.gz	183.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5c0u.ent.gz	143.5 KB	Display	PDB format
PDBx/mmJSON format	5c0u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c0/5c0u ftp://data.pdbj.org/pub/pdb/validation_reports/c0/5c0u	HTTPS FTP

-
Related structure data

Related structure data	5c0tC 5c17C 5dsfC 3f0oS 3f0p C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5u83-2 3f2h-2 5u7b-2 3f0o-1 3hvk-d 3h7d-1 5c0t-1 5uxg-2 3f2f-2 3f0p-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) 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	#122 - Feb 2010 Enhanceosome similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: Alkylmercury lyase

B: Alkylmercury lyase

hetero molecules

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

1

A: Alkylmercury lyase

hetero molecules

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

2

B: Alkylmercury lyase

hetero molecules

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

Unit cell

Length a, b, c (Å)	37.903, 88.958, 52.005
Angle α, β, γ (deg.)	90.000, 100.640, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 1 - 208 / Label seq-ID: 1 - 208

Dom-ID	Selection details	Auth asym-ID	Label asym-ID
1	chain A	A	A
2	chain B	B	B

#1: Protein	Alkylmercury lyase / / Organomercurial lyase Mass: 23030.258 Da / Num. of mol.: 2 / Mutation: D99S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: merB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77072, alkylmercury lyase
#2: Chemical	ChemComp-CU / COPPER (II) ION / Copper Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical	ChemComp-BR / BROMIDE ION / Bromide Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 322 / 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: 1.87 Å³/Da / Density % sol: 34.25 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 23 % polyethylene glycol 2000 MME, 0.2 M sodium acetate pH 5.5, 0.2 M potassium bromide. Before flash freezing, the same precipitant was used except 25 % polyethylene glycol 2000 MME was ...Details: 23 % polyethylene glycol 2000 MME, 0.2 M sodium acetate pH 5.5, 0.2 M potassium bromide. Before flash freezing, the same precipitant was used except 25 % polyethylene glycol 2000 MME was used as a cryo-protectant.

Crystal

Density Matthews: 1.87 Å³/Da / Density % sol: 34.25 %

Crystal grow

Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 23 % polyethylene glycol 2000 MME, 0.2 M sodium acetate pH 5.5, 0.2 M potassium bromide. Before flash freezing, the same precipitant was used except 25 % polyethylene glycol 2000 MME was ...

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL12-2 / Wavelength: 1.376 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2012

Radiation

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

Radiation wavelength

Wavelength: 1.376 Å / Relative weight: 1

Reflection

Redundancy: 3.4 % / Number: 86858 / R_merge(I) obs: 0.052 / Χ²: 1.36 / D res high: 1.87 Å / D res low: 50 Å / Num. obs: 25316 / % possible obs: 90.4

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	ID	R_merge(I) obs	Chi squared	Redundancy
5.07	50	1	0.038	2.042	3.5
4.03	5.07	1	0.038	2.186	3.4
3.52	4.03	1	0.044	2.273	3.5
3.2	3.52	1	0.047	2.141	3.5
2.97	3.2	1	0.05	1.965	3.4
2.79	2.97	1	0.055	1.734	3.5
2.65	2.79	1	0.058	1.606	3.5
2.54	2.65	1	0.061	1.554	3.5
2.44	2.54	1	0.066	1.454	3.4
2.36	2.44	1	0.066	1.249	3.3
2.28	2.36	1	0.069	1.186	3.4
2.22	2.28	1	0.071	1.138	3.4
2.16	2.22	1	0.081	1.064	3.5
2.11	2.16	1	0.083	0.921	3.4
2.06	2.11	1	0.089	0.894	3.4
2.01	2.06	1	0.099	0.886	3.4
1.97	2.01	1	0.1	0.656	3.4
1.94	1.97	1	0.117	0.661	3.4
1.9	1.94	1	0.127	0.552	3.5
1.87	1.9	1	0.143	0.56	3.3

Reflection

Resolution: 1.87→50 Å / Num. obs: 25316 / % possible obs: 90.4 % / Redundancy: 3.4 % / B_iso Wilson estimate: 18.32 Å² / R_merge(I) obs: 0.052 / R_pim(I) all: 0.032 / R_rim(I) all: 0.061 / Χ²: 1.357 / Net I/av σ(I): 28.475 / Net I/σ(I): 12.5 / Num. measured all: 86858

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.87-1.9	3.3	0.143	1039	0.972	0.091	0.17	0.56	74.3
1.9-1.94	3.5	0.127	1252	0.976	0.08	0.15	0.552	90.4
1.94-1.97	3.4	0.117	1312	0.979	0.074	0.139	0.661	94.1
1.97-2.01	3.4	0.1	1320	0.984	0.064	0.12	0.656	92.7
2.01-2.06	3.4	0.099	1258	0.983	0.062	0.117	0.886	92.2
2.06-2.11	3.4	0.089	1240	0.987	0.055	0.105	0.894	88.3
2.11-2.16	3.4	0.083	1153	0.986	0.053	0.099	0.921	83.4
2.16-2.22	3.5	0.081	1285	0.988	0.05	0.095	1.064	91.9
2.22-2.28	3.4	0.071	1321	0.989	0.045	0.085	1.138	95.1
2.28-2.36	3.4	0.069	1313	0.99	0.044	0.082	1.186	92.9
2.36-2.44	3.3	0.066	1273	0.991	0.043	0.079	1.249	92.8
2.44-2.54	3.4	0.066	1258	0.989	0.042	0.079	1.454	87.8
2.54-2.65	3.5	0.061	1198	0.993	0.038	0.072	1.554	87.2
2.65-2.79	3.5	0.058	1333	0.989	0.036	0.068	1.606	95.1
2.79-2.97	3.5	0.055	1319	0.994	0.034	0.065	1.734	94.4
2.97-3.2	3.4	0.05	1287	0.994	0.031	0.059	1.965	91.7
3.2-3.52	3.5	0.047	1225	0.995	0.029	0.055	2.141	87.5
3.52-4.03	3.5	0.044	1347	0.995	0.027	0.051	2.273	94.9
4.03-5.07	3.4	0.038	1236	0.996	0.024	0.045	2.186	88
5.07-50	3.5	0.038	1347	0.997	0.023	0.045	2.042	93

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
HKL-2000		data reduction
PHASER		phasing
PHENIX	1.9_1692	refinement
PDB_EXTRACT	3.15	data extraction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3F0O

3f0o

Resolution: 1.87→31.071 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 19.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1918	3841	7.98 %
R_work	0.147	44309	-
obs	0.1507	48150	87.27 %

Solvent computation

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

Displacement parameters

B_iso max: 110.13 Å² / B_iso mean: 27.5082 Å² / B_iso min: 6.53 Å²

Refinement step

Cycle: final / Resolution: 1.87→31.071 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3174	0	3	322	3499
B_iso mean	-	-	27	34.38	-
Num. residues	-	-	-	-	416

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3279
X-RAY DIFFRACTION	f_angle_d	1.233	4465
X-RAY DIFFRACTION	f_chiral_restr	0.06	527
X-RAY DIFFRACTION	f_plane_restr	0.007	574
X-RAY DIFFRACTION	f_dihedral_angle_d	12.56	1167

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	1726	X-RAY DIFFRACTION	7.835	TORSIONAL
1	2	B	1726	X-RAY DIFFRACTION	7.835	TORSIONAL

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 (%)
1.8702-1.8939	0.2792	107	0.2186	1231	X-RAY DIFFRACTION	65
1.8939-1.9188	0.2294	133	0.1933	1538	X-RAY DIFFRACTION	84
1.9188-1.9451	0.2182	146	0.1623	1709	X-RAY DIFFRACTION	89
1.9451-1.9729	0.2118	147	0.154	1704	X-RAY DIFFRACTION	90
1.9729-2.0023	0.2174	143	0.1603	1661	X-RAY DIFFRACTION	88
2.0023-2.0336	0.2117	145	0.148	1670	X-RAY DIFFRACTION	90
2.0336-2.0669	0.1999	142	0.1548	1652	X-RAY DIFFRACTION	87
2.0669-2.1026	0.2011	143	0.1546	1641	X-RAY DIFFRACTION	85
2.1026-2.1408	0.2169	128	0.1528	1513	X-RAY DIFFRACTION	83
2.1408-2.182	0.253	132	0.1569	1500	X-RAY DIFFRACTION	79
2.182-2.2265	0.1991	146	0.1502	1727	X-RAY DIFFRACTION	91
2.2265-2.2749	0.2356	145	0.1541	1676	X-RAY DIFFRACTION	91
2.2749-2.3278	0.1997	150	0.1559	1724	X-RAY DIFFRACTION	91
2.3278-2.386	0.2319	146	0.1573	1701	X-RAY DIFFRACTION	90
2.386-2.4505	0.2215	141	0.1507	1610	X-RAY DIFFRACTION	87
2.4505-2.5225	0.2451	142	0.1746	1647	X-RAY DIFFRACTION	86
2.5225-2.6039	0.2539	123	0.1689	1433	X-RAY DIFFRACTION	77
2.6039-2.6969	0.1929	154	0.1526	1770	X-RAY DIFFRACTION	93
2.6969-2.8049	0.2378	154	0.1587	1736	X-RAY DIFFRACTION	94
2.8049-2.9324	0.17	154	0.1457	1751	X-RAY DIFFRACTION	92
2.9324-3.0869	0.2016	146	0.1381	1652	X-RAY DIFFRACTION	89
3.0869-3.2801	0.1422	136	0.1435	1561	X-RAY DIFFRACTION	84
3.2801-3.533	0.189	151	0.1398	1707	X-RAY DIFFRACTION	90
3.533-3.888	0.1537	151	0.1331	1780	X-RAY DIFFRACTION	94
3.888-4.4492	0.1659	151	0.1238	1704	X-RAY DIFFRACTION	91
4.4492-5.6001	0.1613	136	0.1295	1622	X-RAY DIFFRACTION	86
5.6001-31.0753	0.1559	149	0.1412	1689	X-RAY DIFFRACTION	90

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	3.7651	0.2322	0.2167	4.4559	-1.3901	3.2163	-0.0564	0.015	-0.0098	-0.0979	0.0825	-0.1578	0.0314	-0.2166	0.0099	0.1538	0.0078	0.0925	0.2528	-0.0066	0.2358	-0.9232	3.932	41.5014
2	1.0861	-0.1239	-0.1668	2.5059	-0.6619	1.7158	-0.4219	-0.0846	-0.1361	1.1239	0.2367	0.1164	0.3857	0.0578	0.0719	0.5487	0.0648	0.0318	0.105	-0.0438	0.2157	12.6637	-14.6763	37.831
3	0.9903	0.2596	-0.0084	0.8698	-0.5471	1.9788	-0.2994	0.0328	0.2837	0.8091	-0.2918	1.1327	0.4358	-0.376	-0.0312	0.3105	-0.0395	0.2335	0.122	-0.1792	0.3465	6.2969	-17.3536	30.7781
4	0.6416	-0.003	0.3385	2.8937	0.064	1.1545	-0.0466	0.1215	-0.1149	-0.035	-0.0341	-0.135	0.0733	0.1457	0.0962	0.1151	0.0135	-0.007	0.0987	-0.015	0.0951	15.7181	-4.0027	26.9795
5	2.0027	-0.7116	0.0764	2.0095	-0.2107	2.3239	-0.0353	-0.0508	-0.0997	0.0736	-0.0294	0.1698	0.09	-0.1411	0.0402	0.081	-0.0084	-0.0003	0.0682	-0.02	0.0762	8.2778	7.473	33.3775
6	3.2151	0.531	0.7264	2.9252	0.5197	2.976	-0.3027	-0.6679	-0.34	-0.1955	0.2283	0.4495	0.1228	0.1677	0.0889	0.23	0.0345	0.0628	0.3216	0.1234	0.2165	4.8071	3.1593	0.4773
7	3.0108	0.694	-1.0923	3.6885	0.1547	4.2845	0.2126	0.3283	-0.1294	-0.586	-0.4151	-0.1324	-0.0818	0.2058	0.137	0.1982	0.0726	-0.0226	0.2299	0.0738	0.1831	3.312	-15.1342	5.6547
8	2.0727	-0.7607	-0.2163	2.7611	0.5151	2.5693	0.2827	0.2635	0.1615	-0.2723	-0.1541	-0.2296	0.068	0.1198	-0.067	0.1015	0.0318	0.0057	0.1346	0.0347	0.1734	8.1086	-20.0723	11.5795
9	1.0656	-1.0619	0.2288	2.8777	-0.2234	1.1397	-0.074	-0.0097	-0.0916	0.1504	0.0712	0.2013	-0.0043	-0.1583	-0.0215	0.103	0.029	0.0072	0.1598	0.0286	0.1065	-4.6458	-10.1511	17.3769
10	1.4599	-0.012	-0.3043	2.964	0.7503	1.5311	0.0791	0.0805	0.0528	0.071	-0.1219	0.3036	0.1075	-0.1241	0.0527	0.0892	0.0284	-0.0058	0.162	0.0182	0.1161	-11.9479	-1.8364	10.7908
11	3.9685	-1.864	0.0674	2.9634	0.3388	1.5845	-0.0364	-0.1002	-0.3489	0.0029	-0.0613	-0.9834	-0.0705	0.666	-0.0311	0.1381	0.0029	0.0851	0.4053	0.0518	0.4007	6.6036	4.2078	8.2425
12	2.0572	-0.2454	-0.1549	1.7042	0.0719	2.1946	-0.0096	0.0701	0.249	-0.131	-0.0884	-0.1903	-0.0576	0.3474	0.0599	0.1247	0.0131	-0.0144	0.2475	0.0708	0.1288	-1.4818	4.6313	7.594

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 14 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 15 through 49 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 50 through 69 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 70 through 96 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 97 through 208 )	A
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 14 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 15 through 33 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 34 through 69 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 70 through 96 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 97 through 141 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 142 through 153 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 154 through 208 )	B

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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