PDB-3zcx: Structure of GAPDH from Thermosynechococcus elongatus

ID or keywords:

Entry

Database: PDB / ID: 3zcx

Title

Structure of GAPDH from Thermosynechococcus elongatus

Components

GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

Keywords

OXIDOREDUCTASE / CALVIN CYCLE / PHOTOSYNTHESIS

Function / homology

Function and homology information

glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glucose metabolic process / NAD binding / NADP binding / metal ion binding
Similarity search - Function

Biological species

THERMOSYNECHOCOCCUS ELONGATUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.19 Å

Authors

Cotton, C.A.R. / Murray, J.W.

Citation

Journal: To be Published
Title: Structure of Gapdh
Authors: Cotton, C.A.R. / Murray, J.W.

History

Deposition	Nov 23, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 11, 2013	Provider: repository / Type: Initial release
Revision 1.1	Feb 5, 2014	Group: Atomic model / Derived calculations / Other
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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 / _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 / _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	3zcx.cif.gz	276.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3zcx.ent.gz	225.6 KB	Display	PDB format
PDBx/mmJSON format	3zcx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3zcx_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	3zcx_full_validation.pdf.gz	1 MB	Display
Data in XML	3zcx_validation.xml.gz	27.8 KB	Display
Data in CIF	3zcx_validation.cif.gz	39 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zc/3zcx ftp://data.pdbj.org/pub/pdb/validation_reports/zc/3zcx	HTTPS FTP

-
Related structure data

Related structure data	3zdfC 4boyC 3b1jS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6gfr-1 6ok4-d 1jn0-1 2d2i-1 3b20-2 2pkr-2 3cmc-d 3cps-3 1gd1-d 3b20-1 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	#50 - Feb 2004 Glycolytic Enzymes similarity (9)

Deposited unit

A: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

B: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

hetero molecules

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

1

A: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

B: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

hetero molecules

A: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

B: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	141.930, 141.930, 76.060
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 0 - 335 / Label seq-ID: 17 - 352

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

NCS oper: (Code: given
Matrix: (-0.9316, 0.08015, -0.3547), (0.05577, -0.9324, -0.3572), (-0.3593, -0.3525, 0.8641)
Vector: 87.41, -73.03, 2.785)

#1: Protein	GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE / GAPDH Mass: 38577.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): KRX References: UniProt: Q8DIW5, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.6 Å³/Da / Density % sol: 53 % / Description: NONE
Crystal grow	Details: 60 MM SODIUM CITRATE PH 5.5, 12% W/V PEG 3000

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.19→76.06 Å / Num. obs: 40432 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.18 % / R_merge(I) obs: 0.09 / Net I/σ(I): 4.61
Reflection shell	Resolution: 2.19→2.25 Å / Redundancy: 6.21 % / R_merge(I) obs: 0.63 / Mean I/σ(I) obs: 1.06 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.7.0032	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B1J

3b1j

Resolution: 2.19→70.96 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.95 / SU B: 9.107 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2084	2025	5 %	RANDOM
R_work	0.16086	-	-	-
obs	0.16319	38354	99.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 44.466 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.35 Å²	0 Å²	0 Å²
2-	-	-0.35 Å²	0 Å²
3-	-	-	0.7 Å²

Refinement step

Cycle: LAST / Resolution: 2.19→70.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5148	0	88	222	5458

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.019	5362
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	5085
X-RAY DIFFRACTION	r_angle_refined_deg	1.933	1.961	7307
X-RAY DIFFRACTION	r_angle_other_deg	1.098	3	11671
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.717	5	677
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.369	24.196	224
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.534	15	874
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.63	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.105	0.2	841
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	6089
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	1221
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.315	2.586	2708
X-RAY DIFFRACTION	r_mcbond_other	2.316	2.586	2707
X-RAY DIFFRACTION	r_mcangle_it	3.349	3.869	3385
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.554	3.009	2654
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 20686 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 2.19→2.247 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.273	142	-
R_work	0.231	2793	-
obs	-	-	99.93 %

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	0.6448	0.0797	0.6866	1.9782	-1.243	1.9285	0.0238	0.1061	0.0181	-0.159	-0.0383	-0.2921	0.0692	0.0293	0.0145	0.148	0.0135	0.0594	0.1844	0.0526	0.1904	53.071	-19.465	3.103
2	4.3452	-0.854	-0.1832	2.8517	-0.2584	0.0484	0.2575	0.4032	0.3343	-0.4203	-0.2938	-0.1606	0.0256	0.04	0.0362	0.258	0.03	0.0939	0.2543	0.0942	0.1993	55.977	-17.426	0.442
3	4.8285	2.5194	1.6284	1.8249	0.2822	1.2957	-0.0817	-0.2215	0.0882	-0.2978	-0.1175	-0.0115	0.1847	0.0798	0.1992	0.2321	-0.0038	0.0535	0.2612	0.0491	0.2015	55.857	-31.654	5.969
4	15.3965	3.2838	9.6209	5.6591	3.5846	18.9717	0.2723	0.435	0.3608	-0.2803	-0.1772	-0.0613	0.8913	0.1226	-0.095	0.1884	0.0086	0.0794	0.1745	0.0793	0.1159	62.364	-27.407	-0.781
5	1.9544	-0.515	0.3323	1.0074	-0.187	0.8873	0.0241	-0.0523	0.3933	0.0476	-0.051	-0.1004	-0.19	0.0805	0.0269	0.1486	-0.0236	0.0134	0.051	0.0287	0.144	48.819	-9.09	9.312
6	3.0807	-1.5974	1.1411	1.3681	-0.453	0.7844	-0.0221	0	0.2483	0.0886	-0.0216	-0.0725	-0.0078	0.0631	0.0437	0.0986	-0.0312	0.0161	0.0998	0.0049	0.0961	35.788	-21.967	21.589
7	1.5461	-4.1699	1.9878	11.4194	-6.0191	5.8907	-0.3112	0.011	0.3252	0.8833	0.0187	-0.8492	-0.4689	0.1065	0.2924	0.1176	-0.0226	-0.0367	0.163	0.0016	0.1628	34.756	-21.796	22.091
8	1.5666	-1.2286	-0.1859	5.3853	-0.1849	0.6085	-0.0322	-0.1794	0.2163	-0.0555	0.104	-0.0448	-0.0166	0.094	-0.0719	0.1246	-0.0341	-0.0242	0.0976	-0.0107	0.1296	31.504	-17.057	15.71
9	4.6404	-2.8139	-1.7816	2.6186	1.2736	2.1607	0.2391	0.2529	0.1109	-0.3249	-0.07	0.2771	-0.1275	-0.3181	-0.1691	0.1205	-0.024	-0.0623	0.1015	0.0534	0.1718	16.221	-16.663	5.983
10	1.0308	0.1617	0.1674	1.0407	-0.3345	0.2202	0.0244	0.1221	0.042	-0.2405	-0.0091	0.0584	0.0287	-0.0114	-0.0153	0.155	0.0061	-0.0147	0.0923	0.0133	0.0581	31.482	-21.045	3.548
11	0.1254	0.2942	-0.4895	2.0418	-1.3035	1.9286	-0.0327	0.0142	-0.0135	0.2339	-0.0095	0.014	0.0651	-0.0491	0.0422	0.0691	-0.0138	0.0099	0.038	0.0276	0.029	50.2811	-19.7334	15.1133
12	0.6867	-0.0358	-0.472	1.8889	1.3162	1.2701	-0.1116	0.1059	0.0002	-0.1838	0.0779	0.1575	0.0331	0.0456	0.0337	0.3046	0.0206	-0.0291	0.1931	-0.0494	0.1546	34.909	-53.775	-6.348
13	7.3042	-0.4546	-6.8308	14.7495	3.5259	13.5736	0.0507	0.3573	-0.0541	-0.8619	-0.1418	-0.8304	-0.2472	0.1161	0.091	0.3565	0.0409	-0.0338	0.439	0.0086	0.2272	41.44	-51.462	-14.7
14	1.2768	0.5907	-0.0261	1.5006	1.2983	1.6276	-0.0097	0.1601	0.1198	-0.257	-0.1203	0.0976	-0.1319	-0.106	0.13	0.3079	0.0203	-0.0249	0.2379	-0.0159	0.165	29.302	-47.081	-3.149
15	2.267	1.2652	-0.9322	8.7824	-1.0861	5.1702	-0.0298	0.3256	0.092	-0.7431	-0.1231	0.2321	-0.3162	-0.1076	0.1528	0.1864	0.0022	-0.0368	0.1964	-0.0925	0.113	25.474	-51.168	-8.44
16	4.744	-0.4931	1.5013	0.7758	0.3398	1.0769	0.1067	0.076	-0.4394	-0.0764	-0.0096	-0.0087	0.2602	0.0313	-0.0972	0.3229	0.0136	0.0409	0.1165	-0.0658	0.1987	36.57	-67.023	-4.639
17	4.2969	-0.5867	1.6789	0.6461	-0.4935	1.4396	-0.003	0.1377	-0.457	-0.1297	-0.0324	-0.1674	0.2239	0.184	0.0353	0.2619	0.0878	0.0706	0.1788	-0.0621	0.2439	55.066	-64.745	3.293
18	3.9802	-0.4626	-1.5913	0.399	-0.0299	0.8798	-0.092	0.0073	-0.1054	-0.0469	0.0333	-0.0065	0.2155	-0.0162	0.0587	0.1993	0.0189	0.0189	0.1379	-0.0077	0.1116	38.874	-54.697	19.36
19	0.6896	-1.0045	-0.5915	4.0546	0.9657	1.4128	0.0148	0.1241	-0.2666	-0.1615	-0.0514	0.2237	0.1197	-0.0539	0.0366	0.223	0.0441	0.014	0.2025	-0.0275	0.2698	50.396	-61.822	11.644
20	2.0031	-1.0303	0.407	1.7688	0.0354	0.914	-0.0202	0.1575	-0.0473	-0.1243	-0.062	-0.2359	0.1191	0.1894	0.0822	0.1423	0.0312	0.0931	0.1736	0.0257	0.1631	62.684	-52.876	4.193
21	2.281	0.1256	0.8817	0.8018	0.3162	1.1333	-0.021	0.0835	-0.2079	-0.1898	0.0012	-0.1401	0.119	0.1025	0.0198	0.1951	0.0396	0.0726	0.1245	-0.0194	0.1327	53.716	-55.836	2.54
22	6.829	2.1731	5.2072	2.0698	2.7359	4.8151	0.2731	-0.4723	0.0092	-0.047	-0.1948	-0.0806	0.1133	-0.3791	-0.0783	0.0549	-0.0229	0.0179	0.0454	-0.0076	0.012	33.6308	-57.1418	4.7366

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 22
2	X-RAY DIFFRACTION	2	A	23 - 40
3	X-RAY DIFFRACTION	3	A	41 - 55
4	X-RAY DIFFRACTION	4	A	57 - 72
5	X-RAY DIFFRACTION	5	A	73 - 166
6	X-RAY DIFFRACTION	6	A	167 - 203
7	X-RAY DIFFRACTION	7	A	204 - 218
8	X-RAY DIFFRACTION	8	A	219 - 244
9	X-RAY DIFFRACTION	9	A	245 - 265
10	X-RAY DIFFRACTION	10	A	266 - 336
11	X-RAY DIFFRACTION	11	A	1000
12	X-RAY DIFFRACTION	12	B	0 - 20
13	X-RAY DIFFRACTION	13	B	21 - 29
14	X-RAY DIFFRACTION	14	B	30 - 55
15	X-RAY DIFFRACTION	15	B	57 - 85
16	X-RAY DIFFRACTION	16	B	86 - 144
17	X-RAY DIFFRACTION	17	B	145 - 175
18	X-RAY DIFFRACTION	18	B	176 - 208
19	X-RAY DIFFRACTION	19	B	209 - 244
20	X-RAY DIFFRACTION	20	B	245 - 292
21	X-RAY DIFFRACTION	21	B	293 - 336
22	X-RAY DIFFRACTION	22	B	1000

-
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