PDB-4aq4: substrate bound sn-glycerol-3-phosphate binding periplasmic prote...

ID or keywords:

Entry

Database: PDB / ID: 4aq4

Title

substrate bound sn-glycerol-3-phosphate binding periplasmic protein ugpB from Escherichia coli

Components

SN-GLYCEROL-3- ...

Keywords

DIESTER-BINDING PROTEIN

Function / homology

Function and homology information

glycerophosphodiester transmembrane transport / glycerol-3-phosphate-transporting ATPase complex / glycerol-3-phosphate transmembrane transport / transmembrane transport / outer membrane-bounded periplasmic space / periplasmic space / membrane
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Wuttge, S. / Bommer, M. / Jaeger, F. / Martins, B.M. / Jacob, S. / Licht, A. / Scheffel, F. / Dobbek, H. / Schneider, E.

Citation

Journal: Mol.Microbiol. / Year: 2012
Title: Determinants of Substrate Specificity and Biochemical Properties of the Sn-Glycerol-3-Phosphate ATP Binding Cassette Transporter (Ugpb-Aec(2) ) of Escherichia Coli.
Authors: Wuttge, S. / Bommer, M. / Jager, F. / Martins, B.M. / Jacob, S. / Licht, A. / Scheffel, F. / Dobbek, H. / Schneider, E.

History

Deposition	Apr 13, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 17, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jul 17, 2013	Group: Database references
Revision 1.2	Mar 6, 2019	Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3	May 8, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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	4aq4.cif.gz	184.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4aq4.ent.gz	147.3 KB	Display	PDB format
PDBx/mmJSON format	4aq4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4aq4_validation.pdf.gz	444.3 KB	Display	wwPDB validaton report
Full document	4aq4_full_validation.pdf.gz	444.4 KB	Display
Data in XML	4aq4_validation.xml.gz	19.5 KB	Display
Data in CIF	4aq4_validation.cif.gz	29.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/aq/4aq4 ftp://data.pdbj.org/pub/pdb/validation_reports/aq/4aq4	HTTPS FTP

-
Related structure data

Similar structure data	7c0u-1 7c0o-1 7c0f-1 7c0l-2 6i5w-d 5l0v-d 7c0v-1 7c14-1 7c15-1 4h3q-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	#205 - Jan 2017 Nuclear Pore Complex similarity (3) #221 - May 2018 Human Papillomavirus and Vaccines similarity (3) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (3) #104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

A: SN-GLYCEROL-3-PHOSPHATE-BINDING PERIPLASMIC PROTEIN UGPB

hetero molecules

47.1 kDa, 1 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)	49.346, 49.346, 406.894
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

-
SN-GLYCEROL-3- ... , 1 types, 1 molecules A

#1: Protein	SN-GLYCEROL-3-PHOSPHATE-BINDING PERIPLASMIC PROTEIN UGPB Mass: 46588.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PFSA131 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AG81, UniProt: P0AG80*PLUS

#1: Protein

SN-GLYCEROL-3-PHOSPHATE-BINDING PERIPLASMIC PROTEIN UGPB

Mass: 46588.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PFSA131 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AG81, UniProt: P0AG80*PLUS

-
Non-polymers , 6 types, 341 molecules

#2: Chemical	ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₉O₆P
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CD / CADMIUM ION Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#5: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Sequence details	THE CRYSTAL STRUCTURE DESCRIBES THE MATURE PROTEIN LACKING THE PERIPLASMIC SIGNAL SEQUENCE.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.67 Å³/Da / Density % sol: 54 % / Description: NONE
Crystal grow	Method: vapor diffusion / pH: 7.5 Details: VAPOUR DIFFUSION (1:1 MIX): 5 MM COBALT(II) CHLORIDE, 5 MM NICKEL(II) CHLORIDE, 5 MM CADMIUM CHLORIDE, 5 MM MAGNESIUM CHLORIDE, 0.1 M HEPES PH 7.5, 12% W/V POLYETHYLENE GLYCOL 3350, 0.3% N- ...Details: VAPOUR DIFFUSION (1:1 MIX): 5 MM COBALT(II) CHLORIDE, 5 MM NICKEL(II) CHLORIDE, 5 MM CADMIUM CHLORIDE, 5 MM MAGNESIUM CHLORIDE, 0.1 M HEPES PH 7.5, 12% W/V POLYETHYLENE GLYCOL 3350, 0.3% N-OCTYL-BETA-D-GLUCOSIDE, 5MM SN- GLYCEROL-3-PHOSPHATE, 1% GLYCEROL, 90 MG/ML PROTEIN

Crystal

Density Matthews: 2.67 Å³/Da / Density % sol: 54 % / Description: NONE

Crystal grow

Method: vapor diffusion / pH: 7.5
Details: VAPOUR DIFFUSION (1:1 MIX): 5 MM COBALT(II) CHLORIDE, 5 MM NICKEL(II) CHLORIDE, 5 MM CADMIUM CHLORIDE, 5 MM MAGNESIUM CHLORIDE, 0.1 M HEPES PH 7.5, 12% W/V POLYETHYLENE GLYCOL 3350, 0.3% N- ...

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1

Diffraction source

Source	Site	Beamline	ID	Wavelength
SYNCHROTRON	BESSY	14.1	1	0.91841
SYNCHROTRON	BESSY	14.2	2	1.9

Detector

Type	ID	Detector	Date
MARMOSAIC 225 mm CCD	1	CCD	Jan 18, 2011
MARMOSAIC 225 mm CCD	2	CCD

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2		M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.91841	1
2	1.9	1

Reflection

Resolution: 1.8→50 Å / Num. obs: 88817 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 5.1 % / B_iso Wilson estimate: 19.59 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 18.8

Reflection shell

Resolution: 1.8→1.91 Å / Redundancy: 5 % / R_merge(I) obs: 0.4 / Mean I/σ(I) obs: 3.9 / % possible all: 98.5

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XDS		data scaling
PHENIX	AUTOSOL	phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 1.8→46.372 Å / SU ML: 0.33 / σ(F): 2 / Phase error: 15.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1922	4464	5 %
R_work	0.1626	-	-
obs	0.1641	88812	99.75 %

Solvent computation

Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 38.633 Å² / k_sol: 0.346 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.1376 Å²	0 Å²	0 Å²
2-	-	1.1376 Å²	0 Å²
3-	-	-	-2.2751 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→46.372 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3274	0	25	335	3634

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3397
X-RAY DIFFRACTION	f_angle_d	1.019	4598
X-RAY DIFFRACTION	f_dihedral_angle_d	13.615	1258
X-RAY DIFFRACTION	f_chiral_restr	0.07	476
X-RAY DIFFRACTION	f_plane_restr	0.004	601

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 (%)
1.7996-1.82	0.2705	138	0.2347	2622	X-RAY DIFFRACTION	93
1.82-1.8414	0.2558	151	0.2201	2844	X-RAY DIFFRACTION	100
1.8414-1.8639	0.2313	145	0.2012	2774	X-RAY DIFFRACTION	100
1.8639-1.8875	0.2345	150	0.195	2867	X-RAY DIFFRACTION	100
1.8875-1.9123	0.2246	145	0.1951	2774	X-RAY DIFFRACTION	100
1.9123-1.9385	0.2476	150	0.1793	2860	X-RAY DIFFRACTION	100
1.9385-1.9662	0.187	152	0.1704	2793	X-RAY DIFFRACTION	100
1.9662-1.9956	0.2092	145	0.1749	2837	X-RAY DIFFRACTION	100
1.9956-2.0267	0.212	145	0.1713	2783	X-RAY DIFFRACTION	100
2.0267-2.06	0.2227	156	0.1713	2866	X-RAY DIFFRACTION	100
2.06-2.0955	0.1636	148	0.165	2748	X-RAY DIFFRACTION	100
2.0955-2.1336	0.2033	151	0.1652	2860	X-RAY DIFFRACTION	100
2.1336-2.1746	0.2021	151	0.1631	2818	X-RAY DIFFRACTION	100
2.1746-2.219	0.1735	146	0.1554	2783	X-RAY DIFFRACTION	100
2.219-2.2673	0.2501	155	0.1658	2842	X-RAY DIFFRACTION	100
2.2673-2.32	0.1908	154	0.1643	2797	X-RAY DIFFRACTION	100
2.32-2.378	0.1978	143	0.163	2819	X-RAY DIFFRACTION	100
2.378-2.4423	0.1896	150	0.1632	2850	X-RAY DIFFRACTION	100
2.4423-2.5142	0.2203	147	0.1596	2820	X-RAY DIFFRACTION	100
2.5142-2.5953	0.1608	152	0.1593	2841	X-RAY DIFFRACTION	100
2.5953-2.6881	0.2113	151	0.163	2839	X-RAY DIFFRACTION	100
2.6881-2.7957	0.1904	147	0.1714	2754	X-RAY DIFFRACTION	100
2.7957-2.9229	0.2039	148	0.1616	2854	X-RAY DIFFRACTION	100
2.9229-3.077	0.2047	147	0.1584	2830	X-RAY DIFFRACTION	100
3.077-3.2697	0.1873	145	0.1609	2806	X-RAY DIFFRACTION	100
3.2697-3.5221	0.1594	149	0.1525	2822	X-RAY DIFFRACTION	100
3.5221-3.8764	0.177	154	0.1428	2793	X-RAY DIFFRACTION	100
3.8764-4.4369	0.1449	155	0.1389	2834	X-RAY DIFFRACTION	100
4.4369-5.5885	0.189	145	0.1551	2806	X-RAY DIFFRACTION	100
5.5885-46.3876	0.1893	149	0.1725	2812	X-RAY DIFFRACTION	100

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	0.7821	-0.3815	-0.2995	0.6416	0.3114	0.7945	-0.0877	0.0057	-0.1371	0.1023	0.0427	-0.0462	0.267	0.1705	0.0265	0.1363	0.0336	0.0595	0.16	-0.0302	0.1466	56.5121	15.0927	168.9063
2	1.0868	-0.0874	-0.6785	0.4545	0.2267	1.1955	0.0404	0.164	0.0536	-0.0001	-0.0415	0.0582	-0.108	-0.0915	-0.0395	0.0981	0.0035	0.0652	0.134	-0.01	0.1418	46.1498	26.3792	167.7283
3	0.7557	0.6208	-0.379	0.56	-0.1536	0.6858	-0.0273	0.0098	-0.0567	0.1224	-0.0867	0.2779	0.1912	-0.3342	-0.421	0.2	-0.082	0.1617	0.3021	-0.0856	0.3058	21.7137	18.5614	189.2584
4	0.8364	-0.0048	-0.2844	0.645	0.4759	0.9237	0.0025	-0.106	0.0216	0.1637	-0.0534	0.1073	0.0189	-0.1185	-0.0086	0.1531	0.0012	0.0904	0.1779	-0.0244	0.151	36.0492	28.293	187.1106
5	0.8914	0.4014	-0.2549	0.5215	-0.3456	1.5245	-0.0294	0.1068	-0.0448	0.0213	-0.0666	0.1532	0.0721	-0.2988	0.0178	0.1307	-0.0275	0.0864	0.1957	-0.052	0.1936	30.8049	19.8122	179.7796
6	0.9111	-0.1426	-0.5391	0.4487	0.1501	0.7795	0.0366	0.0763	0.0275	-0.0728	0.027	-0.0753	-0.0465	0.089	0.0568	0.0802	0.0029	0.0675	0.1639	-0.0204	0.1397	56.4811	22.2427	161.3362
7	1.3167	0.3477	-0.0741	1.0457	0.1219	1.7022	-0.0248	0.3019	-0.0603	-0.0822	-0.092	0.1422	0.0282	-0.231	0.0272	0.1078	-0.0239	0.0369	0.2244	-0.0593	0.1783	37.1541	16.1143	162.3939
8	0.6226	-0.2034	-0.4762	0.7329	0.2868	1.2423	0.0464	0.0218	0.0931	0.044	-0.021	-0.0037	-0.2029	-0.0556	-0.0687	0.1226	0.0076	0.0708	0.1552	-0.0371	0.1697	40.5922	32.7899	181.4422

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ -1:55)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 56:135)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 136:159)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 160:242)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 243:282)
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESSEQ 283:309)
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESSEQ 310:336)
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESSEQ 337:414)

-
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://pdbjlvh1.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

-
SN-GLYCEROL-3- ... , 1 types, 1 molecules A

-
Non-polymers , 6 types, 341 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

-SN-GLYCEROL-3- ... , 1 types, 1 molecules A

-Non-polymers , 6 types, 341 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

-
SN-GLYCEROL-3- ... , 1 types, 1 molecules A

-
Non-polymers , 6 types, 341 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