PDB-7vza: The crystal structure of Non-hydrolyzing UDPGlcNAc 2-epimerase in...

ID or keywords:

Entry

Database: PDB / ID: 7vza

Title

The crystal structure of Non-hydrolyzing UDPGlcNAc 2-epimerase in complex with UDP

Components

Putative UDP-N-acetylglucosamine 2-epimerase

Keywords

ISOMERASE / Epimerase / UDP-sugars

Function / homology

UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) / UDP-N-acetylglucosamine 2-epimerase WecB-like / UDP-N-acetylglucosamine 2-epimerase activity / UDP-N-acetylglucosamine 2-epimerase domain / UDP-N-acetylglucosamine 2-epimerase / nucleotide binding / URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)

Function and homology information

Biological species

Streptomyces kasugaensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.58 Å

Authors

Li, T.L. / Rattinam, R.

Funding support

Taiwan, 1items

Citation

Journal: Biomedicines / Year: 2022
Title: KasQ an Epimerase Primes the Biosynthesis of Aminoglycoside Antibiotic Kasugamycin and KasF/H Acetyltransferases Inactivate Its Activity.
Authors: Rattinam, R. / Basha, R.S. / Wang, Y.L. / Wang, Z.C. / Hsu, N.S. / Lin, K.H. / Zadeh, S.M. / Adhikari, K. / Lin, J.P. / Li, T.L.

History

Deposition	Nov 15, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 16, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jun 7, 2023	Group: Database references / Refinement description / Structure summary Category: audit_author / citation ...audit_author / citation / citation_author / struct_ncs_dom_lim Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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
Revision 1.2	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7vza.cif.gz	576.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7vza.ent.gz	456.7 KB	Display	PDB format
PDBx/mmJSON format	7vza.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7vza_validation.pdf.gz	5.4 MB	Display	wwPDB validaton report
Full document	7vza_full_validation.pdf.gz	5.4 MB	Display
Data in XML	7vza_validation.xml.gz	99.3 KB	Display
Data in CIF	7vza_validation.cif.gz	135.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vz/7vza ftp://data.pdbj.org/pub/pdb/validation_reports/vz/7vza	HTTPS FTP

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Related structure data

Related structure data	7vyyC 7vz6C 1vgvS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Putative UDP-N-acetylglucosamine 2-epimerase

B: Putative UDP-N-acetylglucosamine 2-epimerase

C: Putative UDP-N-acetylglucosamine 2-epimerase

D: Putative UDP-N-acetylglucosamine 2-epimerase

E: Putative UDP-N-acetylglucosamine 2-epimerase

F: Putative UDP-N-acetylglucosamine 2-epimerase

G: Putative UDP-N-acetylglucosamine 2-epimerase

H: Putative UDP-N-acetylglucosamine 2-epimerase

hetero molecules

333 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative UDP-N-acetylglucosamine 2-epimerase

B: Putative UDP-N-acetylglucosamine 2-epimerase

G: Putative UDP-N-acetylglucosamine 2-epimerase

hetero molecules

C: Putative UDP-N-acetylglucosamine 2-epimerase

E: Putative UDP-N-acetylglucosamine 2-epimerase

hetero molecules

D: Putative UDP-N-acetylglucosamine 2-epimerase

hetero molecules

F: Putative UDP-N-acetylglucosamine 2-epimerase

H: Putative UDP-N-acetylglucosamine 2-epimerase

hetero molecules

defined by author&software
333 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	81.820, 104.770, 106.314
Angle α, β, γ (deg.)	74.536, 73.051, 68.390
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 0 - 374 / Label seq-ID: 1 - 375

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30
16	Local NCS retraints between domains: 31 32
17	Local NCS retraints between domains: 33 34
18	Local NCS retraints between domains: 35 36
19	Local NCS retraints between domains: 37 38
20	Local NCS retraints between domains: 39 40
21	Local NCS retraints between domains: 41 42
22	Local NCS retraints between domains: 43 44
23	Local NCS retraints between domains: 45 46
24	Local NCS retraints between domains: 47 48
25	Local NCS retraints between domains: 49 50
26	Local NCS retraints between domains: 51 52
27	Local NCS retraints between domains: 53 54
28	Local NCS retraints between domains: 55 56

#1: Protein	Putative UDP-N-acetylglucosamine 2-epimerase Mass: 41208.227 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces kasugaensis (bacteria) / Gene: kasQ / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K1H2R6
#2: Chemical	ChemComp-UDP / URIDINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₉H₁₄N₂O₁₂P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.36 Å³/Da / Density % sol: 47.8 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M lithium sulfate, 0.1M Bis tris pH5.5, 25% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Apr 27, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.58→19.895 Å / Num. obs: 91395 / % possible obs: 94.1 % / Redundancy: 2.4 % / R_rim(I) all: 0.05 / Net I/σ(I): 23.8
Reflection shell	Resolution: 2.6→2.68 Å / Num. unique obs: 91395 / R_rim(I) all: 0.05

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Processing

Software

Name	Version	Classification
PHENIX	v1.0	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1VGV

1vgv

Resolution: 2.58→19.895 Å / Cor.coef. F_o:F_c: 0.932 / Cor.coef. F_o:F_c free: 0.897 / SU B: 13.216 / SU ML: 0.271 / Cross valid method: NONE / ESU R Free: 0.341
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2488	4644	5.081 %
R_work	0.2098	86751	-
all	0.212	-	-
obs	-	91395	93.946 %

Solvent computation

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

Displacement parameters

B_iso mean: 45.239 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.417 Å²	-0.312 Å²	0.101 Å²
2-	-	-0.371 Å²	0.044 Å²
3-	-	-	-0.098 Å²

Refinement step

Cycle: LAST / Resolution: 2.58→19.895 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22203	0	208	334	22745

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	22791
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	22167
X-RAY DIFFRACTION	r_angle_refined_deg	1.454	1.66	30982
X-RAY DIFFRACTION	r_angle_other_deg	1.18	1.578	50781
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.468	5	2848
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.582	19.405	1310
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.815	15	3732
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.649	15	293
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	2983
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	25425
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5189
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	4444
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.183	0.2	20281
X-RAY DIFFRACTION	r_nbtor_refined	0.146	0.2	10798
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	11222
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.175	0.2	533
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.064	0.2	7
X-RAY DIFFRACTION	r_metal_ion_refined	0.012	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.166	0.2	93
X-RAY DIFFRACTION	r_nbd_other	0.215	0.2	323
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.165	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	3.362	4.573	11494
X-RAY DIFFRACTION	r_mcbond_other	3.362	4.573	11493
X-RAY DIFFRACTION	r_mcangle_it	5.185	6.849	14308
X-RAY DIFFRACTION	r_mcangle_other	5.185	6.85	14309
X-RAY DIFFRACTION	r_scbond_it	3.624	5.068	11297
X-RAY DIFFRACTION	r_scbond_other	3.624	5.069	11296
X-RAY DIFFRACTION	r_scangle_it	5.845	7.417	16674
X-RAY DIFFRACTION	r_scangle_other	5.844	7.417	16675
X-RAY DIFFRACTION	r_lrange_it	8.399	53.541	23588
X-RAY DIFFRACTION	r_lrange_other	8.4	53.55	23558
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.061	0.05	11165
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.067	0.05	11008
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.057	0.05	11207
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.064	0.05	11066
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.063	0.05	11153
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.071	0.05	11078
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.066	0.05	11102
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.058	0.05	11073
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.065	0.05	11149
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.065	0.05	11155
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.063	0.05	11100
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.067	0.05	11022
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.067	0.05	11118
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.068	0.05	11021
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.068	0.05	10985
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.063	0.05	10987
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.07	0.05	10962
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.074	0.05	10947
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.068	0.05	11050
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.057	0.05	11142
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.06	0.05	11077
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.071	0.05	11080
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.064	0.05	11015
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.074	0.05	10990
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.066	0.05	10994
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.068	0.05	11073
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.068	0.05	11115
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.076	0.05	10943

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.0609	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.0609	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06744	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.06744	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.05737	0.05009
3	6	D	X-RAY DIFFRACTION	Local ncs	0.05737	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.06403	0.05009
4	8	E	X-RAY DIFFRACTION	Local ncs	0.06403	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.06321	0.05009
5	10	F	X-RAY DIFFRACTION	Local ncs	0.06321	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.07108	0.05009
6	12	G	X-RAY DIFFRACTION	Local ncs	0.07108	0.05009
7	13	A	X-RAY DIFFRACTION	Local ncs	0.06576	0.05009
7	14	H	X-RAY DIFFRACTION	Local ncs	0.06576	0.05009
8	15	B	X-RAY DIFFRACTION	Local ncs	0.05841	0.05009
8	16	C	X-RAY DIFFRACTION	Local ncs	0.05841	0.05009
9	17	B	X-RAY DIFFRACTION	Local ncs	0.06476	0.05009
9	18	D	X-RAY DIFFRACTION	Local ncs	0.06476	0.05009
10	19	B	X-RAY DIFFRACTION	Local ncs	0.0653	0.05009
10	20	E	X-RAY DIFFRACTION	Local ncs	0.0653	0.05009
11	21	B	X-RAY DIFFRACTION	Local ncs	0.06292	0.05009
11	22	F	X-RAY DIFFRACTION	Local ncs	0.06292	0.05009
12	23	B	X-RAY DIFFRACTION	Local ncs	0.0668	0.05009
12	24	G	X-RAY DIFFRACTION	Local ncs	0.0668	0.05009
13	25	B	X-RAY DIFFRACTION	Local ncs	0.06698	0.05009
13	26	H	X-RAY DIFFRACTION	Local ncs	0.06698	0.05009
14	27	C	X-RAY DIFFRACTION	Local ncs	0.0684	0.05009
14	28	D	X-RAY DIFFRACTION	Local ncs	0.0684	0.05009
15	29	C	X-RAY DIFFRACTION	Local ncs	0.06835	0.05009
15	30	E	X-RAY DIFFRACTION	Local ncs	0.06835	0.05009
16	31	C	X-RAY DIFFRACTION	Local ncs	0.06311	0.05009
16	32	F	X-RAY DIFFRACTION	Local ncs	0.06311	0.05009
17	33	C	X-RAY DIFFRACTION	Local ncs	0.07004	0.05009
17	34	G	X-RAY DIFFRACTION	Local ncs	0.07004	0.05009
18	35	C	X-RAY DIFFRACTION	Local ncs	0.07363	0.05009
18	36	H	X-RAY DIFFRACTION	Local ncs	0.07363	0.05009
19	37	D	X-RAY DIFFRACTION	Local ncs	0.06774	0.05009
19	38	E	X-RAY DIFFRACTION	Local ncs	0.06774	0.05009
20	39	D	X-RAY DIFFRACTION	Local ncs	0.05684	0.05009
20	40	F	X-RAY DIFFRACTION	Local ncs	0.05684	0.05009
21	41	D	X-RAY DIFFRACTION	Local ncs	0.05998	0.05009
21	42	G	X-RAY DIFFRACTION	Local ncs	0.05998	0.05009
22	43	D	X-RAY DIFFRACTION	Local ncs	0.07078	0.05009
22	44	H	X-RAY DIFFRACTION	Local ncs	0.07078	0.05009
23	45	E	X-RAY DIFFRACTION	Local ncs	0.06436	0.05009
23	46	F	X-RAY DIFFRACTION	Local ncs	0.06436	0.05009
24	47	E	X-RAY DIFFRACTION	Local ncs	0.07401	0.05009
24	48	G	X-RAY DIFFRACTION	Local ncs	0.07401	0.05009
25	49	E	X-RAY DIFFRACTION	Local ncs	0.06645	0.05009
25	50	H	X-RAY DIFFRACTION	Local ncs	0.06645	0.05009
26	51	F	X-RAY DIFFRACTION	Local ncs	0.06826	0.05009
26	52	G	X-RAY DIFFRACTION	Local ncs	0.06826	0.05009
27	53	F	X-RAY DIFFRACTION	Local ncs	0.06817	0.05009
27	54	H	X-RAY DIFFRACTION	Local ncs	0.06817	0.05009
28	55	G	X-RAY DIFFRACTION	Local ncs	0.07641	0.05009
28	56	H	X-RAY DIFFRACTION	Local ncs	0.07641	0.05009

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 (%)
2.58-2.6	0.34	197	0.307	4114	X-RAY DIFFRACTION	59.6843
2.6-2.647	0.199	103	0.162	1858	X-RAY DIFFRACTION	98.8906
2.647-2.68	0.275	49	0.251	830	X-RAY DIFFRACTION	79.4756
2.68-2.719	0.323	303	0.296	5426	X-RAY DIFFRACTION	81.6562
2.719-2.798	0.327	333	0.284	6001	X-RAY DIFFRACTION	93.106
2.798-2.884	0.339	303	0.271	6192	X-RAY DIFFRACTION	98.0821
2.884-2.978	0.311	323	0.265	5958	X-RAY DIFFRACTION	98.3096
2.978-3.083	0.309	307	0.254	5804	X-RAY DIFFRACTION	98.3741
3.083-3.199	0.289	327	0.237	5585	X-RAY DIFFRACTION	98.5169
3.199-3.33	0.276	256	0.231	5435	X-RAY DIFFRACTION	98.6309
3.33-3.478	0.276	298	0.222	5129	X-RAY DIFFRACTION	98.3865
3.478-3.647	0.261	283	0.228	4958	X-RAY DIFFRACTION	98.7564
3.647-3.844	0.284	239	0.225	4697	X-RAY DIFFRACTION	98.6608
3.844-4.077	0.218	204	0.213	4536	X-RAY DIFFRACTION	98.6267
4.077-4.358	0.191	216	0.163	4181	X-RAY DIFFRACTION	99.0985
4.358-4.706	0.174	239	0.141	3847	X-RAY DIFFRACTION	98.7434
4.706-5.154	0.182	223	0.147	3595	X-RAY DIFFRACTION	99.3495
5.154-5.761	0.217	162	0.172	3272	X-RAY DIFFRACTION	99.1912
5.761-6.648	0.248	152	0.184	2899	X-RAY DIFFRACTION	99.3487
6.648-8.134	0.195	127	0.172	2434	X-RAY DIFFRACTION	99.3791

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-Yorodumi

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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

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Yorodumi