PDB-2xxj: Penta mutant of lactate dehydrogenase from Thermus thermophilus, ...

ID or keywords:

Entry

Database: PDB / ID: 2xxj

Title

Penta mutant of lactate dehydrogenase from Thermus thermophilus, ternary complex

Components

L-LACTATE DEHYDROGENASE

Keywords

OXIDOREDUCTASE / HYPERTHERMOPHILE

Function / homology

Function and homology information

L-lactate dehydrogenase / L-lactate dehydrogenase activity / glycolytic process / cytoplasm
Similarity search - Function

Biological species

THERMUS THERMOPHILUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.964 Å

Authors

Tickle, J. / de Mendoza Barbera, E. / Vellieux, F.M.D.

Citation

Journal: To be Published
Title: Lactate Dehydrogenase from T. Thermophilus, Penta- Mutant (Ternary Complex)
Authors: Tickle, J. / De Mendoza Barbera, E. / Vellieux, F.M.D.

History

Deposition	Nov 10, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 24, 2010	Provider: repository / Type: Initial release
Revision 1.1	Aug 3, 2011	Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Other / Version format compliance
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_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_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	2xxj.cif.gz	473.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2xxj.ent.gz	392 KB	Display	PDB format
PDBx/mmJSON format	2xxj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2xxj_validation.pdf.gz	1008.9 KB	Display	wwPDB validaton report
Full document	2xxj_full_validation.pdf.gz	1 MB	Display
Data in XML	2xxj_validation.xml.gz	51.2 KB	Display
Data in CIF	2xxj_validation.cif.gz	73.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xx/2xxj ftp://data.pdbj.org/pub/pdb/validation_reports/xx/2xxj	HTTPS FTP

-
Related structure data

Related structure data	2v7pS 2v6m 2xxb 4a73 S: Starting model for refinement
Similar structure data	3pqd-1 4m1q-1 3wsw-d 4nd5-2 3vph-d 6isi-d 4v4e-10 1hyh-d 4okn-1 2e37-2 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	#102 - Jun 2008 Lactate Dehydrogenase similarity (11) #154 - Oct 2012 Citric Acid Cycle similarity (6) #142 - Oct 2011 PDB Pioneers similarity (10)

Deposited unit

A: L-LACTATE DEHYDROGENASE

B: L-LACTATE DEHYDROGENASE

C: L-LACTATE DEHYDROGENASE

D: L-LACTATE DEHYDROGENASE

hetero molecules

132 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)	57.150, 147.360, 152.280
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	L-LACTATE DEHYDROGENASE / L-LDH Mass: 32599.373 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PTTHLDH12 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): DH5ALPHA / References: UniProt: Q5SJA1, L-lactate dehydrogenase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-OXM / OXAMIC ACID Mass: 89.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃NO₃
#4: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 643 / 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: 2.46 Å³/Da / Density % sol: 49.97 % / Description: NONE
Crystal grow	pH: 6.5 Details: 0.1M NACACODYLATE 0.2M NAAC PH 6.5, 15% W/V PEG 8000. DROPLETS = 2.0 MICROL PROTEIN, 2 MICROL PRECIPITANT, 0.5 MICROL ADDITIVE (30% D(PLUS)-GLUCOSE MONOHYDRATE).

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.97245
Detector	Type: ADSC CCD / Detector: CCD / Date: Jan 31, 2010 / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97245 Å / Relative weight: 1
Reflection	Resolution: 1.96→105.9 Å / Num. obs: 91523 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 7.37 % / B_iso Wilson estimate: 25.04 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 20.94
Reflection shell	Resolution: 1.96→2.08 Å / Redundancy: 4.91 % / R_merge(I) obs: 0.44 / Mean I/σ(I) obs: 3.32 / % possible all: 93.4

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V7P

2v7p

Resolution: 1.964→67.644 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 21.56 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2263	4577	5 %
R_work	0.1752	-	-
obs	0.1777	91516	98.89 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 29.659 Å² / k_sol: 0.335 e/Å³

Displacement parameters

B_iso mean: 29.13 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.0938 Å²	0 Å²	0 Å²
2-	-	-4.0562 Å²	0 Å²
3-	-	-	-0.0376 Å²

Refinement step

Cycle: LAST / Resolution: 1.964→67.644 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9175	0	110	643	9928

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	9541
X-RAY DIFFRACTION	f_angle_d	1.137	13038
X-RAY DIFFRACTION	f_dihedral_angle_d	16.317	3523
X-RAY DIFFRACTION	f_chiral_restr	0.107	1540
X-RAY DIFFRACTION	f_plane_restr	0.005	1685

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 (%)
1.9643-2.0346	0.2831	426	0.2424	7711	X-RAY DIFFRACTION	89
2.0346-2.116	0.2855	473	0.2049	8694	X-RAY DIFFRACTION	100
2.116-2.2123	0.2573	479	0.1884	8648	X-RAY DIFFRACTION	100
2.2123-2.329	0.2586	431	0.1815	8726	X-RAY DIFFRACTION	100
2.329-2.4749	0.2474	440	0.1747	8751	X-RAY DIFFRACTION	100
2.4749-2.666	0.2282	448	0.1704	8741	X-RAY DIFFRACTION	100
2.666-2.9343	0.2371	431	0.1824	8797	X-RAY DIFFRACTION	100
2.9343-3.3589	0.2349	475	0.183	8830	X-RAY DIFFRACTION	100
3.3589-4.2317	0.2017	448	0.1598	8900	X-RAY DIFFRACTION	100
4.2317-67.6841	0.1871	526	0.149	9141	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	0.4505	-0.3345	-0.0166	0.4527	0.1116	0.4176	-0.0052	0.0053	0.095	0.1116	0.0063	-0.0952	-0.0492	0.0827	0.0039	0.0302	-0.0011	-0.0137	0.0438	0.0242	0.1298	17.8574	24.6668	31.6706
2	0.7584	0.0708	-0.0666	0.2318	0.5475	1.3924	-0.0371	0.0365	0.2159	-0.2566	0.066	0.1456	-0.6827	0.076	-0.0271	0.3735	-0.0349	-0.0048	0.1215	0.0941	0.3569	20.2158	36.9166	15.6662
3	0.2963	0.1923	-0.217	0.4117	0.0331	0.2966	0.0933	0.1523	-0.0446	-0.1689	-0.0904	0.0022	-0.0185	-0.1115	-0.0157	0.0701	-0.0328	0.0279	0.0615	0.1028	-0.0113	11.5067	15.2988	8.5023
4	0.1198	-0.0475	-0.1935	0.3256	0.0916	0.3118	-0.018	0.1335	-0.0104	-0.1343	-0.0806	0.0584	-0.1539	-0.2906	0.0594	0.2137	0.0574	-0.0322	0.3528	0.0496	0.1331	-4.5917	9.8901	0.7421
5	0.5295	0.4219	-0.331	0.3354	-0.263	0.2065	0.213	0.3708	0.144	-0.1588	-0.3207	-0.015	-0.1873	-0.0552	0.0848	0.3935	0.1027	-0.1125	0.2611	0.0743	0.2153	-2.1059	26.5068	11.407
6	0.8732	-0.1748	-0.1735	0.7241	-0.481	0.3863	0.0658	0.0567	0.052	-0.053	-0.0414	-0.0601	0.0728	0.125	0.0488	0.0867	-0.0214	0.0144	0.1116	0.0364	0.0582	17.8097	16.0383	10.7599
7	0.6424	0.645	-0.071	1.7237	-0.5064	0.189	-0.0567	0.4469	0.0266	-0.3737	0.0625	0.0875	0.1089	-0.0576	-0.0998	0.1772	0.0194	0.119	0.1108	0.3396	-0.1224	16.4254	25.3643	-3.3312
8	0.2235	0.3416	-0.1714	0.5508	-0.3494	0.5644	-0.044	0.0956	0.0231	-0.1285	0.0819	0.0863	0.0779	-0.0694	-0.0562	0.0597	-0.0181	-0.0391	0.0937	0.0512	0.0802	-3.2138	18.3246	26.1018
9	0.0604	-0.0855	-0.1283	0.6233	-0.3182	0.5638	-0.0378	0.0468	0.0417	0.0113	0.1475	0.2388	-0.0258	-0.1861	-0.1097	0.021	0.0081	-0.0065	0.0795	0.0704	0.1619	-12.0269	24.5098	40.3698
10	0.0095	-0.0039	0.0106	0.8775	-0.267	0.095	-0.0132	-0.0302	-0.0073	0.053	0.0407	-0.1569	-0.0635	-0.0337	-0.0027	0.07	0.0009	-0.0124	0.04	0.0281	0.0892	12.6759	20.174	52.3466
11	0.6324	-0.4924	0.2099	0.8338	-0.5762	0.4481	-0.1272	0.0624	0.251	0.2797	-0.0651	-0.469	-0.1855	0.0315	0.1306	0.214	-0.0259	-0.0778	0.108	0.0469	0.3543	23.443	25.224	56.566
12	0.5777	-0.4103	0.4288	0.3017	-0.1738	1.405	-0.0537	0.0257	0.1867	0.1339	-0.097	-0.1803	-0.4123	0.0309	0.1414	0.104	-0.0118	-0.002	0.019	0.0296	0.1892	9.482	33.5973	46.4862
13	0.2053	-0.03	0.004	0.8285	-0.0783	0.2848	0.0456	0.0166	-0.0269	0.134	0.0615	0.0036	0.0721	-0.0136	-0.0729	0.0364	0.0036	-0.0046	0.0362	0.0416	0.0673	-2.1027	17.5154	49.9165
14	0.2097	-0.1609	0.0159	0.3284	1.1735	6.6418	0.0278	-0.0815	-0.0138	0.1092	-0.0887	-0.0172	-0.2588	-0.5242	0.0441	0.1329	0.027	0.0502	0.0686	0.026	0.1031	-7.1316	30.9838	59.5173
15	0.3183	-0.1624	-0.0419	0.1947	0.1042	0.5234	-0.0498	0.0663	0.0057	0.015	0.0183	-0.0396	0.0145	0.0545	0.0211	0.0803	-0.0157	0.0189	0.078	-0.0062	0.0718	26.1123	-7.1773	27.8694
16	0.5195	-0.3963	-0.2436	0.3098	0.1505	0.8582	-0.1225	-0.0618	-0.1156	0.1628	0.1528	0.0742	0.419	0.1626	-0.0016	0.2959	0.0966	0.0114	0.1305	0.013	0.1635	34.8902	-20.8001	45.4568
17	0.5173	-0.1766	-0.3183	0.2183	0.2603	0.5669	-0.0848	0.0338	0.1217	0.0892	0.0993	-0.0517	0.1571	0.0207	-0.0104	0.0513	0.0141	-0.017	0.0287	0.0154	0.0516	21.2889	-1.6966	50.3001
18	1.4047	-0.6651	-0.3967	2.1484	-0.4285	0.7227	-0.0667	0.0027	-0.1415	0.1402	0.1352	-0.0077	0.2939	-0.0188	0.0022	0.1222	-0.029	-0.005	0.0047	0.0304	0.0412	5.9174	-6.8122	60.5258
19	0.6867	-0.2557	-0.0857	0.3511	0.5025	0.8498	0.0136	0.0666	-0.1078	0.3012	0.024	0.0633	0.2267	0.1285	-0.0469	0.137	0.0062	0	0.0507	-0.0032	0.0545	17.962	-9.2668	41.5943
20	0.434	-0.236	0.0039	0.9399	-0.238	0.1808	-0.0139	-0.0464	0.1911	0.1365	0.0421	-0.0609	-0.0111	0.0336	0.0243	0.0542	-0.0057	-0.0174	0.0449	-0.0352	0.0069	27.2072	3.8641	53.3873
21	0.9146	-0.5079	0.4493	1.024	-0.6183	0.4897	-0.0156	-0.267	0.024	0.4084	-0.0637	0.0008	0.0692	0.1177	0.0206	0.2233	0.0524	-0.0668	0.1399	0.0227	0.0681	30.4314	-7.8765	62.2301
22	0.4001	0.0307	0.0599	0.5406	0.0118	0.2153	0.0057	-0.0187	0.0834	0.3098	-0.0667	0.1684	-0.0028	-0.0045	0.0442	0.1235	-0.0223	0.0752	0.0476	-0.0197	0.075	3.4927	-13.482	35.9376
23	0.4583	0.3502	0.2036	0.4349	0.0089	0.2194	0.0284	0.3133	-0.1252	-0.0064	0.0062	-0.0876	0.0286	0.1949	-0.0669	0.1083	0.0008	0.0478	0.2412	-0.0485	0.2089	15.1559	-29.6752	21.4131
24	0.4732	0.0512	0.1717	0.5685	-0.2785	0.1146	-0.0417	0.2001	-0.0255	-0.0957	0.0814	0.1047	0.0598	0.0308	-0.0218	0.0526	-0.0311	0.051	0.0999	-0.0305	0.0359	6.3401	-16.2331	15.1941
25	0.589	0.0851	-0.431	0.3907	-0.3321	0.5071	-0.0882	0.2485	0.0369	-0.1246	-0.0014	-0.0836	0.1266	-0.2842	0.0364	0.2206	-0.0231	0.0954	0.2093	0.0268	0.1791	26.1007	-3.3728	1.4627
26	0.2272	0.2983	-0.2881	1.1228	-0.554	0.4067	-0.0516	0.0169	-0.0373	-0.1211	0.0334	-0.1544	0.0525	-0.0997	0.038	0.1156	-0.023	0.0495	0.1592	-0.0585	0.1249	22.1811	-19.0507	13.3873
27	0.7082	0.217	0.3193	1.0437	0.2733	0.1572	-0.1005	0.2453	-0.0527	-0.0997	0.054	0.1293	-0.1232	0.0383	0.0419	0.0548	-0.0461	0.0368	0.1486	-0.0122	0.0123	2.527	-11.7685	13.4841
28	0.7305	0.4041	0.2508	1.3555	1.369	1.417	-0.1038	0.4408	-0.241	-0.1963	0.2719	-0.1492	0.0599	0.2023	-0.1446	0.1081	-0.0754	0.0141	0.0987	-0.2237	-0.0518	4.3316	-25.0981	3.2606

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 1:74)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 75:108)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 109:194)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 195:213)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 214:222)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 223:288)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 289:310)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 1:57)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 58:141)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 142:194)
11	X-RAY DIFFRACTION	11	(CHAIN B AND RESID 195:208)
12	X-RAY DIFFRACTION	12	(CHAIN B AND RESID 209:222)
13	X-RAY DIFFRACTION	13	(CHAIN B AND RESID 223:290)
14	X-RAY DIFFRACTION	14	(CHAIN B AND RESID 291:309)
15	X-RAY DIFFRACTION	15	(CHAIN C AND RESID 1:75)
16	X-RAY DIFFRACTION	16	(CHAIN C AND RESID 76:99)
17	X-RAY DIFFRACTION	17	(CHAIN C AND RESID 100:194)
18	X-RAY DIFFRACTION	18	(CHAIN C AND RESID 195:217)
19	X-RAY DIFFRACTION	19	(CHAIN C AND RESID 218:243)
20	X-RAY DIFFRACTION	20	(CHAIN C AND RESID 244:288)
21	X-RAY DIFFRACTION	21	(CHAIN C AND RESID 289:310)
22	X-RAY DIFFRACTION	22	(CHAIN D AND RESID 1:75)
23	X-RAY DIFFRACTION	23	(CHAIN D AND RESID 76:83)
24	X-RAY DIFFRACTION	24	(CHAIN D AND RESID 84:189)
25	X-RAY DIFFRACTION	25	(CHAIN D AND RESID 190:206)
26	X-RAY DIFFRACTION	26	(CHAIN D AND RESID 207:222)
27	X-RAY DIFFRACTION	27	(CHAIN D AND RESID 223:288)
28	X-RAY DIFFRACTION	28	(CHAIN D AND RESID 289:310)

-
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