PDB-6k94: Crystal structure of the type III effector XopAI from Xanthomonas...

ID or keywords:

Entry

Database: PDB / ID: 6k94

Title

Crystal structure of the type III effector XopAI from Xanthomonas axonopodis pv. citri - a 70 residue N-terminal truncation

Components

Type III effector XopAI

Keywords

CELL INVASION / type III effectors / peptide-binding domain / mono-ADP-ribosyltransferase fold / Xanthomonas axonopodis pv. citri

Function / homology

Function and homology information

cellular anatomical structure / NAD+-protein-arginine ADP-ribosyltransferase / NAD+-protein-arginine ADP-ribosyltransferase activity / nucleotidyltransferase activity
Similarity search - Function

Biological species

Xanthomonas citri (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.26 Å

Authors

Liu, J.-H. / Li, Y.-P. / Yang, J.-Y. / Hou, M.-H.

Funding support

Taiwan, 1items

Citation

Journal: Int J Mol Sci / Year: 2019
Title: Crystal Structure-Based Exploration of Arginine-Containing Peptide Binding in the ADP-Ribosyltransferase Domain of the Type III Effector XopAI Protein.
Authors: Liu, J.H. / Yang, J.Y. / Hsu, D.W. / Lai, Y.H. / Li, Y.P. / Tsai, Y.R. / Hou, M.H.

History

Deposition	Jun 14, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 30, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6k94.cif.gz	555.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6k94.ent.gz	448.6 KB	Display	PDB format
PDBx/mmJSON format	6k94.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6k94_validation.pdf.gz	462.4 KB	Display	wwPDB validaton report
Full document	6k94_full_validation.pdf.gz	468.6 KB	Display
Data in XML	6k94_validation.xml.gz	38.8 KB	Display
Data in CIF	6k94_validation.cif.gz	55.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k9/6k94 ftp://data.pdbj.org/pub/pdb/validation_reports/k9/6k94	HTTPS FTP

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Related structure data

Related structure data	6k93C 6klyC 4eln PDB Unreleased entryS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5thx-d 1h8o-1 2atp-1 3lho-d 3ktz-1 1h8s-1 4m5o-d 6nsl-2 4lna-d 1imf-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) 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

Related structure data

6k93C

6klyC

4eln
PDB Unreleased entryS

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Type III effector XopAI

B: Type III effector XopAI

C: Type III effector XopAI

D: Type III effector XopAI

116 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Type III effector XopAI

defined by author
Evidence: equilibrium centrifugation
29 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Type III effector XopAI

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

3

C: Type III effector XopAI

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

4

D: Type III effector XopAI

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

Unit cell

Length a, b, c (Å)	62.780, 98.760, 77.450
Angle α, β, γ (deg.)	90.000, 91.210, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb

#1: Protein	Type III effector XopAI Mass: 28961.355 Da / Num. of mol.: 4 / Fragment: 70 residue N-terminal truncation Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas citri (bacteria) / Strain: XW19 / Gene: XopAI, XAC3230 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL+ / References: UniProt: Q8PHM1
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 558 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Type III effector XopAI

Mass: 28961.355 Da / Num. of mol.: 4 / Fragment: 70 residue N-terminal truncation
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Xanthomonas citri (bacteria) / Strain: XW19 / Gene: XopAI, XAC3230 / Plasmid: pET28a / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL+ / References: UniProt: Q8PHM1

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 558 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.06 Å³/Da / Density % sol: 40.32 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 10% (v/v) 2-propanol, 20% (w/v) PEG400, and 100 mM HEPES-NaOH, pH 9.5

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Data collection

Diffraction	Mean temperature: 110 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9762 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 2.26→31.53 Å / Num. obs: 44030 / % possible obs: 99.4 % / Redundancy: 3.5 % / B_iso Wilson estimate: 20.919 Å² / CC_1/2: 0.99 / R_merge(I) obs: 0.142 / R_pim(I) all: 0.088 / R_rim(I) all: 0.167 / Χ²: 0.89 / Net I/σ(I): 7.5
Reflection shell	Resolution: 2.26→2.33 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.783 / Num. unique obs: 4034 / CC_1/2: 0.609 / R_pim(I) all: 0.482 / R_rim(I) all: 0.922 / Χ²: 0.8 / % possible all: 99.3

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
iMOSFLM	v7.2.2	data reduction
pointless	v1.11.21	data scaling
PHASER	v2.8.0	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4eln

4eln
PDB Unreleased entry

Resolution: 2.26→31.527 Å / Cross valid method: FREE R-VALUE / Phase error: 23.55

	R_factor	Num. reflection	% reflection
R_free	0.2319	2222	5.05 %
R_work	0.1893	-	-
obs	0.1915	44004	99.36 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 35.06 Å²

Refinement step

Cycle: LAST / Resolution: 2.26→31.527 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7354	0	0	558	7912

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	0.0945	0.0061	-0.0104	0.0392	0.0314	0.0225	-0.0324	-0.2231	-0.0276	0.014	-0.1071	0.2311	-0.0687	-0.0422	-0.0047	0.2126	0.0334	-0.0189	0.2831	-0.079	0.2302	-3.3279	6.2568	10.4381
2	0.0234	0.0277	0.006	0.0413	0.032	0.0419	0.0102	-0.018	-0.0286	0.0048	-0.0219	0.0004	-0.1891	-0.0747	-0.0001	0.1952	0.0039	-0.0219	0.2328	0.0016	0.1906	-0.6064	0.9993	-4.4036
3	0.0853	-0.1072	-0.1127	0.1241	0.1235	0.1612	-0.0522	0.1181	-0.0154	0.0387	0.0593	0.0084	-0	-0.0325	0	0.1853	-0.0065	-0.0135	0.1986	-0.025	0.1608	7.5341	-5.4732	-6.8118
4	0.111	-0.0509	-0.1165	0.0867	0.1569	0.2234	0.0061	-0.0653	0.0612	-0.0453	-0.0751	0.0436	0.0453	-0.0187	-0.0003	0.1486	0.0023	-0.0141	0.1502	0.0015	0.1768	8.9246	1.087	7.042
5	0.0088	0.0288	0.0146	0.1133	-0.0071	0.0635	-0.0847	-0.0203	-0.0145	-0.032	-0.0022	0.1716	-0.0975	0.1022	-0	0.1661	-0.0001	-0.0043	0.1503	-0.0068	0.1716	15.4983	9.6443	16.1891
6	0.4604	-0.0932	-0.1167	0.0172	0.0251	0.033	-0.038	0.0171	-0.1853	0.0383	-0.0619	-0.0356	-0.208	0.2497	-0.0176	0.2188	-0.0434	-0.0332	0.2888	0.0167	0.1397	25.371	1.3251	10.3625
7	0.1363	0.0205	-0.0372	0.0076	-0.0363	0.1594	-0.0054	-0.0083	-0.0952	-0.008	-0.0781	-0.0394	-0.0585	-0.0465	-0.0297	0.1279	0.0163	-0.012	0.1423	-0.0129	0.1812	16.9655	-2.2557	10.4677
8	0.146	-0.1628	-0.0867	0.1757	0.0985	0.0569	-0.1733	-0.06	0.0032	0.2543	0.0924	-0.0104	-0.153	-0.0488	-0.0292	0.267	-0.0631	-0.0725	0.2453	0.0152	0.1972	24.1178	6.4962	17.8254
9	0.0694	-0.0396	-0.0289	0.1044	-0.0782	0.0984	-0.0293	-0.002	-0.1561	0.0369	0.0645	0.2503	-0.0304	-0.0323	0.0007	0.1694	-0.0053	0.0218	0.2004	-0.0047	0.3549	3.7094	30.0549	-8.8504
10	0.0718	0.0034	0.0438	0.1187	-0.0362	0.0461	-0.0298	0.036	-0.177	0.1398	0.0003	-0.0855	0.0151	-0.023	0.0134	0.1903	-0.026	0.0405	0.1422	-0.015	0.3486	13.7249	17.9918	-7.9504
11	0.3975	-0.1911	-0.1417	0.2428	-0.1419	0.3455	-0.3248	-0.0233	-0.2085	0.0209	-0.1063	-0.0546	0.1688	0.0101	-0.8667	0.2179	0.1628	0.1834	0.084	0.0462	0.4151	25.1897	13.6591	-8.6981
12	0.3054	0.0778	-0.2085	0.2654	-0.0548	0.1234	-0.0057	0.0759	-0.0293	0.0325	-0.0219	0.0421	-0.0077	0.0078	-0	0.1405	0.0098	-0.0091	0.1391	-0.0066	0.1823	18.4143	33.105	-11.3053
13	0.0704	0.0611	0.0157	0.049	0.0279	0.0141	0.1632	0.0799	0.0324	-0.01	0.0849	-0.0561	-0.0015	0.1124	0.0015	0.2275	0.0191	0.0329	0.2173	-0.002	0.213	29.7959	41.6034	-17.4469
14	0.0613	0.0544	0.0266	0.0467	0.0238	0.1337	-0.0998	-0.1358	-0.0036	-0.0515	0.1373	-0.0391	-0.0289	0.0443	-0.0404	0.1476	0.0291	0.0368	0.2562	0.0526	0.2227	28.2019	31.3325	-6.195
15	0.0187	0.0241	0.0478	0.0236	0.0507	0.1197	-0.0105	0.0609	0.0758	0.112	-0.0104	-0.0203	-0.0427	0.0965	-0.0001	0.1538	0.0041	0.0116	0.1921	0.0314	0.2252	22.3165	41.6015	-11.6786
16	0.4087	0.2212	0.1986	0.1265	0.1094	0.0989	0.1984	-0.0274	-0.0828	-0.1216	-0.1104	-0.0442	0.0671	-0.0565	0.0008	0.2779	0.0672	0.1066	0.1734	0.0576	0.3123	22.7327	48.353	-18.7109
17	1.1002	0.3075	-0.0553	0.088	-0.0195	0.0042	0.0671	-0.3248	0.0731	0.0538	-0.1951	-0.1644	0.0791	0.4225	-0.1022	0.2848	0.0329	-0.055	0.5144	0.2371	0.2776	32.7186	-23.6927	-26.1338
18	0.0309	0.0509	-0.019	0.0692	-0.0437	0.0604	-0.1103	-0.1773	0.0686	-0.1566	-0.2931	-0.0713	0.1322	0.1046	0	0.2485	0.0628	0.0445	0.3479	0.0947	0.3593	30.7235	-17.8019	-40.7232
19	0.0868	0.0645	0.0105	0.0797	0.0374	0.1129	-0.1782	0.078	0.0063	-0.0293	-0.0641	0.1134	-0.0377	0.0621	-0.0116	0.3115	-0.0105	0.0322	0.2778	0.048	0.2586	23.1213	-12.5593	-48.9678
20	0.1809	-0.127	-0.0612	0.1042	-0.0072	0.2134	-0.1299	-0.0563	-0.0215	0.0171	-0.0677	0.1369	0.0957	0.218	-0.0623	0.1685	-0.0369	-0.0139	0.1997	0.0403	0.1547	21.0662	-11.5714	-37.8263
21	0.0508	0.0469	0.0983	0.2626	-0.0377	0.4495	0.1189	0.0097	0.0507	0.0886	-0.1313	0.0687	0.1022	0.1881	-0.0302	0.2465	0.0229	0.0128	0.2339	0.0422	0.1528	18.7209	-21.8758	-29.5761
22	0.0633	0.0751	0.0003	0.078	0.0212	0.1239	0.0467	-0.0012	-0.0318	0.0533	0.0379	-0.041	0.0051	0.0772	0.0771	0.2237	0.027	0.0225	0.1946	0.018	0.1086	15.2416	-27.0478	-21.0504
23	0.0246	-0.0266	-0.0177	0.0326	0.0159	0.0119	-0.1161	0.1087	0.0917	0.0398	0.0865	-0.0593	0.1435	-0.1128	-0	0.2953	-0.0305	0.0184	0.2523	-0.0487	0.1747	3.4266	-21.7788	-28.622
24	0.036	0.0105	-0.0457	0.0759	0.0501	0.0946	-0.0579	0.0529	-0.0102	0.0483	0.0135	0.1337	-0.1819	0.1405	0	0.2418	-0.0108	0.0097	0.2341	0.0379	0.1929	13.3345	-13.5881	-32.1968
25	0.0139	-0.012	0.0023	0.0104	-0.0039	0.0172	0.0178	0.0242	0.0193	0.1141	-0.0871	-0.0493	0.0239	-0.1071	0	0.3502	-0.0318	0.0202	0.3281	0.0486	0.2876	8.3696	-26.3624	-16.1242
26	0.0102	0.0034	-0.0169	0.0157	-0.0296	0.0625	-0.0804	0.0649	-0.2025	0.1408	0.1047	-0.0476	-0.092	-0.0593	0	0.2846	-0.075	-0.0204	0.2916	0.0136	0.2433	4.4803	-27.7536	-21.5534
27	0.0963	0.0169	-0.0202	0.0825	-0.0767	0.0753	-0.1659	-0.0577	0.1521	-0.2292	0.2445	0.3028	-0.0328	-0.004	-0.0015	0.2245	-0.1037	-0.0673	0.4549	0.0907	0.4252	-29	1.1356	-27.5043
28	0.4953	0.1591	-0.5739	0.7089	-0.5549	0.8747	-0.0813	-0.082	0.4564	-0.1859	0.2584	0.0076	0.2352	0.0022	0.0751	0.181	0.0144	-0.1082	0.1828	0.0047	0.4908	-11.6086	14.3442	-30.8908
29	0.6875	0.0774	-0.0286	0.0825	-0.0292	0.268	-0.1059	-0.1827	0.2403	-0.1872	0.1665	0.1125	0.2025	-0.0566	-0.115	0.2068	-0.0292	-0.0763	0.211	0.0407	0.2119	-12.9521	0.2226	-28.2832
30	0.1119	0.0233	-0.0478	0.1176	0.0113	0.0302	-0.2011	-0.1448	0.0499	-0.1203	-0.0123	-0.0012	0.0466	-0.0237	-0.0196	0.1451	-0.0176	-0.0146	0.3791	0.0158	0.1658	-14.2247	-12.0221	-21.0176
31	0.0622	-0.0548	-0.0272	0.0701	0.0478	0.0409	0.0992	-0.0321	-0.3108	-0.0187	-0.1848	-0.1281	-0.0539	0.0104	-0.0003	0.2359	-0.0838	-0.0463	0.2638	0.0481	0.2114	-4.8536	-12.8611	-19.9513
32	0.0647	-0.0604	-0.024	0.0615	-0.0076	0.077	-0.0309	-0.112	0.0846	-0.1303	0.0397	0.01	0.0971	0.0183	-0.0001	0.2642	-0.0131	-0.0037	0.2735	0.0235	0.2184	-6.867	-3.5152	-30.6821
33	-0.0031	-0.0016	0.0067	0.0581	-0.0372	0.016	0.061	-0.0269	-0.1206	0.1107	-0.018	-0.0213	0.0672	-0.0972	-0	0.3037	-0.0853	-0.0361	0.3016	0.0661	0.2373	-10.94	-19.7401	-19.4643

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 73:92 )	A	73 - 92
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 93:112 )	A	93 - 112
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 113:161 )	A	113 - 161
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 162:204 )	A	162 - 204
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 205:230 )	A	205 - 230
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 231:248 )	A	231 - 248
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 249:281 )	A	249 - 281
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 282:296 )	A	282 - 296
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 71:92 )	B	71 - 92
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 93:112 )	B	93 - 112
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 113:136 )	B	113 - 136
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 137:230 )	B	137 - 230
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 231:248 )	B	231 - 248
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 249:260 )	B	249 - 260
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 261:280 )	B	261 - 280
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 281:296 )	B	281 - 296
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 73:92 )	C	73 - 92
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 93:112 )	C	93 - 112
19	X-RAY DIFFRACTION	19	( CHAIN C AND RESID 113:135 )	C	113 - 135
20	X-RAY DIFFRACTION	20	( CHAIN C AND RESID 136:161 )	C	136 - 161
21	X-RAY DIFFRACTION	21	( CHAIN C AND RESID 162:212 )	C	162 - 212
22	X-RAY DIFFRACTION	22	( CHAIN C AND RESID 213:230 )	C	213 - 230
23	X-RAY DIFFRACTION	23	( CHAIN C AND RESID 231:248 )	C	231 - 248
24	X-RAY DIFFRACTION	24	( CHAIN C AND RESID 249:272 )	C	249 - 272
25	X-RAY DIFFRACTION	25	( CHAIN C AND RESID 273:281 )	C	273 - 281
26	X-RAY DIFFRACTION	26	( CHAIN C AND RESID 282:296 )	C	282 - 296
27	X-RAY DIFFRACTION	27	( CHAIN D AND RESID 73:92 )	D	73 - 92
28	X-RAY DIFFRACTION	28	( CHAIN D AND RESID 93:136 )	D	93 - 136
29	X-RAY DIFFRACTION	29	( CHAIN D AND RESID 137:210 )	D	137 - 210
30	X-RAY DIFFRACTION	30	( CHAIN D AND RESID 211:234 )	D	211 - 234
31	X-RAY DIFFRACTION	31	( CHAIN D AND RESID 235:248 )	D	235 - 248
32	X-RAY DIFFRACTION	32	( CHAIN D AND RESID 249:272 )	D	249 - 272
33	X-RAY DIFFRACTION	33	( CHAIN D AND RESID 273:296 )	D	273 - 296

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