PDB-5f7s: Cycloalternan-degrading enzyme from Trueperella pyogenes

ID or keywords:

Entry

Database: PDB / ID: 5f7s

Title

Cycloalternan-degrading enzyme from Trueperella pyogenes

Components

Glycoside hydrolase family 31

Keywords

HYDROLASE /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

hydrolase activity, hydrolyzing O-glycosyl compounds /

carbohydrate binding / carbohydrate metabolic process
Similarity search - Function

Biological species

Trueperella pyogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Light, S.H. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: Nat Microbiol / Year: 2016
Title: Structure to function of an alpha-glucan metabolic pathway that promotes Listeria monocytogenes pathogenesis.
Authors: Light, S.H. / Cahoon, L.A. / Halavaty, A.S. / Freitag, N.E. / Anderson, W.F.

History

Deposition	Dec 8, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 30, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 23, 2016	Group: Database references
Revision 1.2	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_id / _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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5f7s.cif.gz	571.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5f7s.ent.gz	469.9 KB	Display	PDB format
PDBx/mmJSON format	5f7s.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f7/5f7s ftp://data.pdbj.org/pub/pdb/validation_reports/f7/5f7s	HTTPS FTP

-
Related structure data

Related structure data	4kmqSC 5do8C 5f7pC 5f7qC 5f7rC 5f7uC 5f7vC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6phy-d 3d0r-d 5i0e-d 3a6o-1 3weo-d 2p6p-d 2j5t-5 5i5x-d 5te1-1 5i0f-d 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	#198 - Jun 2016 Beta-galactosidase similarity (1) #203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: Glycoside hydrolase family 31

B: Glycoside hydrolase family 31

hetero molecules

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

1

A: Glycoside hydrolase family 31

hetero molecules

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

2

B: Glycoside hydrolase family 31

hetero molecules

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

Unit cell

Length a, b, c (Å)	197.126, 104.663, 89.030
Angle α, β, γ (deg.)	90.00, 90.74, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Glycoside hydrolase family 31 / Mass: 82328.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trueperella pyogenes (bacteria) / Gene: CQ11_05330 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: X4QP62
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 657 / 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: 2.79 Å³/Da / Density % sol: 55.89 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, sitting drop Details: Protein solution: 12.0 mg/ml, 0.5 M NaCl, 0.01 M Tris-HCl pH 8.3 Crystallization condition: PACT (Qiagen) C11: 0.2 M Calcium chloride, 0.1 m Hepes pH 7, and 25% (w/v) PEG 600

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 2.3→30 Å / Num. obs: 80180 / % possible obs: 100 % / Redundancy: 3.8 % / R_merge(I) obs: 0.074 / Net I/σ(I): 15.2
Reflection shell	Resolution: 2.3→2.34 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.564 / Mean I/σ(I) obs: 2.2 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4KMQ

4kmq

Resolution: 2.3→30 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.94 / SU B: 12.291 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21122	4135	5.2 %	RANDOM
R_work	0.16965	-	-	-
obs	0.1718	76044	99.72 %	-

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: 36.376 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.41 Å²	-0 Å²	0.45 Å²
2-	-	-0.28 Å²	0 Å²
3-	-	-	-0.14 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11226	0	36	657	11919

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	11611
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	10414
X-RAY DIFFRACTION	r_angle_refined_deg	1.526	1.927	15836
X-RAY DIFFRACTION	r_angle_other_deg	0.882	3	23909
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.427	5	1398
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.932	22.987	596
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.872	15	1699
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.177	15	102
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	1613
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	13342
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2904
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	1.187	2.364	5607
X-RAY DIFFRACTION	r_mcbond_other	1.185	2.363	5606
X-RAY DIFFRACTION	r_mcangle_it	1.984	3.539	7000
X-RAY DIFFRACTION	r_mcangle_other	1.985	3.54	7001
X-RAY DIFFRACTION	r_scbond_it	1.489	2.581	6004
X-RAY DIFFRACTION	r_scbond_other	1.489	2.581	6004
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.518	3.797	8837
X-RAY DIFFRACTION	r_long_range_B_refined	5.111	19.796	13446
X-RAY DIFFRACTION	r_long_range_B_other	5.111	19.798	13447
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.3→2.359 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.271	293	-
R_work	0.243	5484	-
obs	-	-	97.6 %

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	0.3341	-1.3472	1.0032	12.0675	-4.3871	3.0381	-0.0042	-0.0392	0.0057	0.1083	0.0101	0.263	-0.036	-0.136	-0.0058	0.0713	0.0005	0.0251	0.1366	-0.0152	0.1311	465.4126	27.2465	40.0012
2	2.8777	2.1214	-3.1694	2.4395	-2.0437	4.7996	0.1429	-0.1787	-0.2835	0.31	-0.3396	-0.3503	-0.3569	0.3096	0.1967	0.1308	-0.0588	-0.0157	0.1593	0.0679	0.1389	473.6389	20.079	43.2505
3	1.3937	1.6527	-2.4252	2.5754	-2.7148	4.681	-0.1655	-0.1504	-0.3495	-0.1329	-0.2711	-0.405	0.3605	0.3215	0.4366	0.0375	0.0223	0.0082	0.1723	0.0719	0.2383	476.1253	19.7067	38.5828
4	1.3664	-0.3963	-0.3607	1.8745	0.3382	0.5097	-0.0363	0.0295	-0.0544	-0.0367	-0.0078	-0.2078	0.0388	0.0924	0.044	0.0344	0.0123	0.0257	0.1148	0.0173	0.0454	476.5197	46.2801	26.6487
5	2.4832	-0.9437	-0.3398	1.0707	0.4347	0.3655	-0.0423	0.3409	-0.156	-0.0575	-0.0422	-0.0421	0.0348	-0.0359	0.0845	0.1684	-0.0036	0.0458	0.1897	-0.0035	0.0985	464.2373	51.6581	17.0044
6	1.8053	0.855	0.0186	1.8923	-0.1184	0.2308	-0.0445	0.0423	-0.1436	0.0767	0.0566	0.2971	-0.0285	-0.0945	-0.0121	0.0711	0.0218	0.0339	0.1203	-0.0236	0.1104	433.6879	52.9046	32.3551
7	1.1258	-0.2074	-0.072	3.435	-0.3626	0.5419	-0.0688	0.0938	-0.2967	0.194	-0.0219	0.3996	0.0179	-0.1265	0.0906	0.0302	-0.0206	0.0314	0.0759	-0.0395	0.1501	441.1248	40.5816	30.0617
8	5.968	-4.581	-1.1535	8.7972	4.0783	6.7766	-0.1871	-0.492	-0.3292	0.2778	0.0854	0.2598	0.1475	0.1438	0.1017	0.0279	0.005	0.0066	0.0701	0.0408	0.117	453.0272	30.673	34.0957
9	0.8784	-0.0333	-0.0496	1.1569	0.0683	0.517	-0.0007	0.0377	-0.0431	-0.0094	-0.0512	-0.0422	-0.0597	-0.0063	0.0519	0.056	0.0125	-0.0009	0.1085	0.0005	0.0095	455.5229	57.6804	29.2053
10	4.7379	0.1768	-1.1038	3.8266	-0.7343	1.2932	0.2502	0.2157	0.4274	-0.0698	-0.0958	-0.3834	-0.3616	0.1474	-0.1544	0.1638	-0.0595	0.0262	0.0612	0.0183	0.161	467.1039	80.6828	28.7461
11	1.0642	-0.1109	-0.0767	2.8671	-1.0528	1.318	0.0518	-0.0631	-0.0497	0.1499	-0.1609	0.0941	-0.1894	0.0809	0.1091	0.1249	-0.0062	0.0481	0.1865	0.0405	0.1108	470.4072	26.0257	-6.5573
12	1.6644	0.4254	-3.5117	0.7932	-0.0268	8.5261	-0.1457	-0.2318	-0.1928	0.0806	-0.0695	-0.1805	0.4345	0.4691	0.2152	0.0789	0.0211	0.0242	0.0903	0.0741	0.1378	475.3105	11.8068	-1.0592
13	1.8694	1.6884	-2.6984	2.7255	-3.0117	5.4507	-0.1186	-0.1768	-0.3253	-0.1285	-0.2639	-0.2628	0.2997	0.3368	0.3825	0.0558	0.0236	0.0268	0.1546	0.0928	0.1485	475.3462	17.8084	-6.105
14	2.7152	1.6466	0.0786	5.7987	2.0607	1.4173	-0.0165	0.1066	-0.1243	-0.3228	-0.0513	-0.4191	-0.005	0.1272	0.0677	0.0947	0.0313	0.0586	0.2347	0.0244	0.1677	483.1011	39.1389	-26.7685
15	1.1581	-0.3965	-0.2519	0.7638	0.108	0.2775	-0.0382	0.0463	-0.0518	0.0384	-0.038	-0.0572	0.0066	-0.0081	0.0762	0.0834	-0.0021	0.0135	0.1184	-0.0091	0.0353	460.672	50.581	-18.4335
16	1.0114	-0.4919	-0.2884	1.1474	0.2841	0.7799	-0.0824	0.0112	-0.2051	0.196	-0.0513	0.3151	0.035	-0.2231	0.1337	0.0649	-0.0374	0.0495	0.1449	-0.056	0.1229	436.238	44.8699	-14.3158
17	7.1496	-3.7411	-3.3693	8.1582	6.7287	7.6595	-0.1581	-0.2664	-0.1386	0.092	-0.0197	0.2123	0.2513	0.0437	0.1779	0.0188	0.0142	0.0104	0.0348	0.0309	0.0493	453.4649	30.4226	-11.685
18	0.6316	0.0724	0.0071	0.7843	0.1423	0.5187	-0.0004	-0.0032	-0.0822	0.0863	-0.0705	0.0389	-0.0058	-0.0743	0.0708	0.07	0.0077	0.0083	0.1208	-0.0077	0.0223	452.1541	52.9532	-14.1741
19	6.792	-5.5783	2.7331	4.5834	-2.2628	1.4091	-0.2711	-0.264	-0.2843	0.2438	0.2226	0.2295	-0.2748	-0.1784	0.0486	0.1506	0.0145	-0.0248	0.1024	-0.0437	0.1333	449.9771	75.4051	-16.6572
20	1.8228	-0.4482	-0.5903	1.4954	0.1679	1.0277	0.0943	0.0023	0.296	-0.0854	-0.0613	-0.3133	-0.1437	0.0713	-0.0329	0.077	-0.0121	0.0063	0.0765	0.0257	0.0983	466.6176	73.4398	-19.8024

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 17
2	X-RAY DIFFRACTION	2	A	18 - 50
3	X-RAY DIFFRACTION	3	A	51 - 144
4	X-RAY DIFFRACTION	4	A	145 - 254
5	X-RAY DIFFRACTION	5	A	255 - 300
6	X-RAY DIFFRACTION	6	A	301 - 378
7	X-RAY DIFFRACTION	7	A	379 - 416
8	X-RAY DIFFRACTION	8	A	417 - 432
9	X-RAY DIFFRACTION	9	A	433 - 694
10	X-RAY DIFFRACTION	10	A	695 - 730
11	X-RAY DIFFRACTION	11	B	1 - 38
12	X-RAY DIFFRACTION	12	B	39 - 53
13	X-RAY DIFFRACTION	13	B	54 - 138
14	X-RAY DIFFRACTION	14	B	139 - 172
15	X-RAY DIFFRACTION	15	B	173 - 352
16	X-RAY DIFFRACTION	16	B	353 - 416
17	X-RAY DIFFRACTION	17	B	417 - 431
18	X-RAY DIFFRACTION	18	B	432 - 626
19	X-RAY DIFFRACTION	19	B	627 - 631
20	X-RAY DIFFRACTION	20	B	632 - 730

-
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