PDB-5w15: Crystal structure of an alpha/beta hydrolase fold protein from Bu...

ID or keywords:

Entry

Database: PDB / ID: 5w15

Title

Crystal structure of an alpha/beta hydrolase fold protein from Burkholderia ambifaria.

Components

Alpha/beta hydrolase fold protein

Keywords

HYDROLASE / SSGCID / Burkholderia ambifaria / alpha/beta hydrolase / fold protein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Alpha/beta hydrolase fold protein

Function and homology information

Biological species

Burkholderia ambifaria (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.75 Å

Authors

SSGCID / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of an alpha/beta hydrolase fold protein from Burkholderia ambifaria.
Authors: Irwin, R.M. / Mayclin, S.J. / Lorimer, D. / Edwards, T.E.

History

Deposition	Jun 1, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 14, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jun 28, 2017	Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2	Nov 22, 2017	Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3	Oct 4, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5w15.cif.gz	464.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5w15.ent.gz	379.8 KB	Display	PDB format
PDBx/mmJSON format	5w15.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5w15_validation.pdf.gz	455.7 KB	Display	wwPDB validaton report
Full document	5w15_full_validation.pdf.gz	458.7 KB	Display
Data in XML	5w15_validation.xml.gz	53.2 KB	Display
Data in CIF	5w15_validation.cif.gz	81 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w1/5w15 ftp://data.pdbj.org/pub/pdb/validation_reports/w1/5w15	HTTPS FTP

-
Related structure data

Related structure data	4k2aS S: Starting model for refinement
Similar structure data	4lvh-3 6ag0-d 5lr6-d 6nex-d 2a71-d 3ths-1 6db5-d 6qnl-d 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	#165 - Sep 2013 Designed Protein Cages similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: Alpha/beta hydrolase fold protein

B: Alpha/beta hydrolase fold protein

C: Alpha/beta hydrolase fold protein

D: Alpha/beta hydrolase fold protein

hetero molecules

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

1

A: Alpha/beta hydrolase fold protein

hetero molecules

C: Alpha/beta hydrolase fold protein

hetero molecules

B: Alpha/beta hydrolase fold protein

D: Alpha/beta hydrolase fold protein

hetero molecules

defined by author&software
124 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	60.070, 143.590, 75.850
Angle α, β, γ (deg.)	90.000, 111.340, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Alpha/beta hydrolase fold protein Mass: 30793.957 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia ambifaria (strain MC40-6) (bacteria) Strain: MC40-6 / Gene: BamMC406_3075 / Plasmid: BuamA.00095.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1YPY7
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1363 / 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: 2.48 Å³/Da / Density % sol: 50.4 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 Details: JCGS+ B8 (283558b8): 100 mM Tris-HCl pH 7.0, 200 mM MgCl2, 10% PEG 8000, protein conc. 19. 9mg/mL, cryo 20% ethylene glycol: puck ID vkw3-6

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 22, 2016

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.75→50 Å / Num. obs: 120204 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.082 % / B_iso Wilson estimate: 19.2 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.068 / R_rim(I) all: 0.076 / Χ²: 1.043 / Net I/σ(I): 14.92

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.75-1.8	4.933	0.565	2.73	8866	0.835	0.633	99.9
1.8-1.84	5.083	0.454	3.51	8699	0.887	0.507	99.9
1.84-1.9	5.076	0.346	4.58	8375	0.931	0.387	99.9
1.9-1.96	5.077	0.273	5.83	8174	0.956	0.305	100
1.96-2.02	5.094	0.219	7.18	7903	0.97	0.245	99.8
2.02-2.09	5.097	0.176	8.78	7671	0.979	0.196	99.9
2.09-2.17	5.104	0.141	10.79	7407	0.985	0.157	99.9
2.17-2.26	5.112	0.118	12.57	7084	0.989	0.131	99.8
2.26-2.36	5.116	0.101	14.47	6844	0.992	0.113	99.9
2.36-2.47	5.121	0.086	16.6	6521	0.994	0.096	99.8
2.47-2.61	5.127	0.076	18.73	6237	0.994	0.085	99.9
2.61-2.77	5.124	0.066	21.07	5862	0.996	0.073	99.9
2.77-2.96	5.109	0.058	23.53	5508	0.996	0.065	99.9
2.96-3.2	5.09	0.051	26.34	5172	0.997	0.057	99.7
3.2-3.5	5.08	0.045	29.25	4726	0.998	0.05	100
3.5-3.91	5.069	0.041	31.62	4291	0.998	0.046	99.7
3.91-4.52	5.078	0.037	33.94	3786	0.998	0.042	99.8
4.52-5.53	5.083	0.035	34.41	3215	0.998	0.039	99.7
5.53-7.83	5.077	0.035	33.89	2485	0.998	0.04	99.6
7.83-50	4.902	0.031	35.82	1378	0.998	0.035	98.5

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
Coot		model building
PHENIX		refinement
PDB_EXTRACT	3.22	data extraction
XDS		data scaling
PHENIX		phasing
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4k2a

4k2a

Resolution: 1.75→50 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.71

	R_factor	Num. reflection	% reflection
R_free	0.1878	1970	1.64 %
R_work	0.1659	-	-
obs	0.1662	120149	99.97 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 76.62 Å² / B_iso mean: 24.1322 Å² / B_iso min: 8.67 Å²

Refinement step

Cycle: final / Resolution: 1.75→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8469	0	18	1388	9875
B_iso mean	-	-	35.35	36.57	-
Num. residues	-	-	-	-	1080

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	8968
X-RAY DIFFRACTION	f_angle_d	0.876	12308
X-RAY DIFFRACTION	f_chiral_restr	0.057	1310
X-RAY DIFFRACTION	f_plane_restr	0.006	1641
X-RAY DIFFRACTION	f_dihedral_angle_d	14.826	5307

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work
1.75-1.7937	0.2811	150	0.2559	8414
1.7937-1.8422	0.2543	157	0.2276	8404
1.8422-1.8964	0.2133	149	0.2037	8420
1.8964-1.9576	0.2282	132	0.1976	8423
1.9576-2.0276	0.2073	133	0.1987	8419
2.0276-2.1088	0.2104	169	0.1883	8423
2.1088-2.2047	0.2148	126	0.1813	8426
2.2047-2.321	0.2019	142	0.1731	8449
2.321-2.4664	0.2002	132	0.1744	8439
2.4664-2.6568	0.1863	130	0.1712	8421
2.6568-2.9241	0.1989	139	0.165	8456
2.9241-3.3471	0.1719	130	0.1531	8478
3.3471-4.2164	0.1603	153	0.1361	8461
4.2164-50	0.1508	128	0.1408	8546

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	4.6522	0.1209	-0.0869	4.384	-0.4612	5.4546	0.0932	0.1588	0.233	-0.2541	-0.0249	0.2409	-0.1528	-0.2797	-0.1005	0.1122	-0.0149	-0.0092	0.1433	-0.0282	0.1411	87.7158	-8.3582	-45.349
2	2.0228	0.3793	0.5857	1.7723	-0.0277	1.6634	0.0039	-0.14	0.0633	0.0699	-0.0486	0.0318	0.0311	-0.0579	0.0358	0.1056	0.005	0.0224	0.116	0.0003	0.0779	97.6159	-7.0435	-38.354
3	5.2309	-1.7823	3.7088	2.2663	-1.0898	4.1974	-0.2995	-0.0502	0.1299	0.5206	0.0153	0.4026	-0.5506	-0.447	0.2483	0.4039	0.0876	0.0112	0.3148	-0.0003	0.36	88.332	17.8114	-34.8069
4	2.3445	-0.4826	0.6113	2.0273	-0.3594	1.2624	-0.0225	0.3907	0.2902	-0.2843	-0.0371	0.2354	-0.1579	-0.0748	0.0797	0.2411	0.0315	-0.0508	0.1652	0.0313	0.2231	92.799	11.5657	-48.7372
5	2.1886	-0.4457	0.5159	1.5778	-0.0865	1.0321	-0.0234	-0.2614	0.1389	0.2074	-0.0473	0.0851	-0.1274	-0.0519	0.0444	0.1853	-0.0007	-0.0039	0.1687	-0.0389	0.1274	102.3137	3.2843	-31.8967
6	3.7769	0.6169	2.3154	2.7937	-0.1677	6.9643	-0.014	0.0118	0.0478	0.019	-0.0395	-0.2167	-0.059	0.3848	0.022	0.0816	-0.0207	0.0337	0.1515	0.0052	0.1049	111.3368	-0.127	-44.2373
7	4.7501	-0.5128	0.3077	3.3392	0.9391	3.4615	-0.0269	-0.0496	0.0179	0.0004	0.1003	0.2538	0.2269	-0.273	-0.0035	0.1563	0.0051	-0.0325	0.1394	0.028	0.1247	113.3038	-21.8344	-19.7688
8	2.399	0.0484	0.5678	1.6554	-0.1895	1.8806	-0.0983	0.0654	0.126	-0.0623	0.0425	-0.089	-0.0824	0.0407	0.0497	0.132	-0.0124	-0.0025	0.1081	0.0206	0.1015	124.67	-23.5545	-16.8619
9	2.2805	0.5947	1.2494	3.2885	1.7834	2.5361	-0.2687	0.3898	0.0034	-0.4074	0.2191	-0.3857	-0.2031	0.2768	0.0616	0.2752	-0.0754	0.034	0.2054	-0.0075	0.2205	120.34	-45.5424	-27.8657
10	2.4707	1.0067	1.2401	1.6334	0.6155	2.4853	-0.1415	0.1498	0.0602	-0.2255	0.0781	-0.0741	0.0677	0.1256	0.0703	0.1524	0.0298	0.0294	0.087	0.001	0.1343	126.1756	-33.4246	-20.1347
11	5.5351	1.5743	-0.9656	2.5158	-0.599	2.1684	-0.0564	-0.0233	-0.3771	0.0311	0.0311	-0.4213	0.2024	0.1641	0.0188	0.1404	0.0342	-0.0267	0.1517	0.0062	0.1627	132.6929	-34.9143	-7.6334
12	2.7688	1.0201	-1.7507	3.7082	-0.2032	7.4268	0.2066	0.0652	0.5411	0.238	-0.1127	-0.2424	-0.4413	-0.0114	-0.0788	0.1245	-0.0268	0.0051	0.1823	0.0171	0.2749	101.579	6.0482	8.541
13	1.5056	-0.2576	-0.0691	2.4141	0.0863	1.2444	0.0277	0.0928	0.0528	-0.0205	-0.0089	-0.1897	-0.0112	0.1228	-0.0035	0.065	0.002	0.0115	0.1512	0.0057	0.1293	97.7707	-2.9139	5.5112
14	2.4662	-0.4127	-0.396	3.2867	0.185	1.7699	0.1555	0.3768	-0.0635	-0.278	-0.1002	0.0958	0.0512	0.0287	0.0207	0.1243	0.0274	0.0158	0.1654	-0.0211	0.1322	92.1153	-11.2584	-0.3997
15	2.4163	-1.6825	0.3031	2.8214	-0.0644	2.4768	0.5831	0.5776	-0.3478	-0.9703	-0.5384	-0.1581	0.1286	0.2282	0.0969	0.4427	0.1476	0.018	0.3195	0.0369	0.3688	86.4067	11.0169	-14.8541
16	1.1174	-0.4128	0.1805	3.6488	-0.4191	0.7145	0.0889	0.2183	0.114	-0.1839	-0.072	-0.0434	-0.1099	-0.0238	-0.0041	0.1252	0.0246	0.0145	0.1876	0.0248	0.1389	88.0782	6.7605	-4.4856
17	1.6419	-0.3983	-0.0815	3.7427	-0.1127	0.9897	0.081	0.094	-0.2098	-0.276	0.0262	0.275	-0.0211	-0.0552	-0.0743	0.1653	0.0053	-0.0297	0.1815	-0.0273	0.1541	83.307	-13.214	-0.3346
18	1.7104	1.1889	-0.5936	4.6703	3.1954	4.0588	0.0392	-0.036	-0.0199	0.2133	0.0203	0.0451	0.1475	0.069	-0.0778	0.0674	-0.0004	0.0198	0.1359	0.0105	0.1068	81.9977	-8.2827	9.5661
19	4.3458	0.1141	-3.7535	4.5098	-2.0081	7.3763	0.0381	-0.0349	-0.4745	-0.0951	-0.0558	-0.1527	0.5858	0.0305	0.0217	0.2101	0.0224	-0.0739	0.161	0.0422	0.2386	126.2422	-45.4192	19.3148
20	1.3651	-0.0182	0.1659	1.805	0.3062	1.3447	0.0691	-0.1009	-0.1768	0.2031	-0.0626	0.0794	0.1443	-0.0041	-0.0122	0.1446	-0.0183	-0.0033	0.1196	0.0325	0.1097	116.6137	-38.0723	19.4307
21	1.2944	-0.0135	0.2843	2.159	0.1863	0.7939	0.0736	-0.0221	-0.238	0.0698	-0.0664	0.2366	0.1506	-0.0794	0.0117	0.1339	-0.0205	0.0136	0.1497	0.0111	0.1771	107.7043	-40.1248	14.7276
22	3.1504	-3.1854	-1.5985	3.4915	0.9429	2.5653	0.1085	0.0834	0.116	-0.283	-0.1113	-0.0891	-0.0676	0.0707	0.0333	0.1095	0.0007	-0.0088	0.1425	0.0257	0.0829	113.6588	-28.4881	6.0346

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -2 through 20 )	A	-2 - 20
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 21 through 130 )	A	21 - 130
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 131 through 147 )	A	131 - 147
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 148 through 181 )	A	148 - 181
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 182 through 237 )	A	182 - 237
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 238 through 267 )	A	238 - 267
7	X-RAY DIFFRACTION	7	chain 'B' and (resid -2 through 20 )	B	-2 - 20
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 21 through 130 )	B	21 - 130
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 131 through 162 )	B	131 - 162
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 163 through 219 )	B	163 - 219
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 220 through 267 )	B	220 - 267
12	X-RAY DIFFRACTION	12	chain 'C' and (resid -2 through 20 )	C	-2 - 20
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 21 through 108 )	C	21 - 108
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 109 through 130 )	C	109 - 130
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 131 through 147 )	C	131 - 147
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 148 through 206 )	C	148 - 206
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 207 through 237 )	C	207 - 237
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 238 through 267 )	C	238 - 267
19	X-RAY DIFFRACTION	19	chain 'D' and (resid -2 through 20 )	D	-2 - 20
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 21 through 147 )	D	21 - 147
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 148 through 237 )	D	148 - 237
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 238 through 267 )	D	238 - 267

-
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