PDB-4z9c: EcPltAB Oxidized

ID or keywords:

Entry

Database: PDB / ID: 4z9c

Title

EcPltAB Oxidized

Components

Pertussis toxin-like subunit ArtA
Subtilase cytotoxin subunit B-like protein

Keywords

TRANSFERASE / Redox switch / Pertussis toxin / Typhoid toxin / ADP-ribosyltransferase / Escherichia coli / AB5

Function / homology

Function and homology information

NAD+ poly-ADP-ribosyltransferase activity / ribosome / structural constituent of ribosome / translation / nucleotide binding / extracellular region
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Littler, D.R. / Johnson, M.D. / Summers, R.J. / Schembri, M.A. / Rossjohn, J. / Beddoe, T.

Citation

Journal: J. Biol. Chem. / Year: 2017
Title: Structure and function analyses of a pertussis-like toxin from pathogenic Escherichia coli reveal a distinct mechanism of inhibition of trimeric G proteins.
Authors: Littler, D.R. / Ang, S.Y. / Moriel, D.G. / Kocan, M. / Kleifeld, O. / Johnson, M.D. / Tran, M.T. / Paton, A.W. / Paton, J.C. / Summers, R. / Schrembri, M. / Rossjohn, J. / Beddoe, T.T.

History

Deposition	Apr 10, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 12, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 9, 2017	Group: Data collection / Database references / Derived calculations Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Sep 27, 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
Revision 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4z9c.cif.gz	343.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4z9c.ent.gz	283 KB	Display	PDB format
PDBx/mmJSON format	4z9c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4z9c_validation.pdf.gz	491.8 KB	Display	wwPDB validaton report
Full document	4z9c_full_validation.pdf.gz	506.6 KB	Display
Data in XML	4z9c_validation.xml.gz	30.1 KB	Display
Data in CIF	4z9c_validation.cif.gz	41 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z9/4z9c ftp://data.pdbj.org/pub/pdb/validation_reports/z9/4z9c	HTTPS FTP

-
Related structure data

Related structure data	4z9dC 3dwaS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3g0d-4 2q62-2 4bp9-5 1uby-2 4l72-1 1l1l-3 3g0g-3 1e60-1 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	#69 - Sep 2005 Cholera Toxin similarity (2)

Deposited unit

A: Pertussis toxin-like subunit ArtA

B: Subtilase cytotoxin subunit B-like protein

C: Subtilase cytotoxin subunit B-like protein

D: Subtilase cytotoxin subunit B-like protein

E: Subtilase cytotoxin subunit B-like protein

F: Subtilase cytotoxin subunit B-like protein

hetero molecules

101 kDa, 6 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)	160.900, 160.900, 62.640
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	Pertussis toxin-like subunit ArtA / Pertussis-like toxin subunit A Mass: 27565.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PU15_14675, PU38_26245 / Details (production host): pUC57 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0B1KWV6, NAD+ ADP-ribosyltransferase
#2: Protein	Subtilase cytotoxin subunit B-like protein / Pertussis-like toxin subunit B Mass: 14683.417 Da / Num. of mol.: 5 / Fragment: UNP residues 25-141 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PU15_14670, PU38_26240 / Plasmid: pUC57 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0B1KTJ4
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.32 Å³/Da / Density % sol: 46.94 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, 15% w/v PEG3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.35→49.42 Å / Num. obs: 38825 / % possible obs: 99.9 % / Redundancy: 8.4 % / R_merge(I) obs: 0.041 / Net I/σ(I): 12.1
Reflection shell	Resolution: 2.35→2.48 Å / Redundancy: 8.1 % / R_merge(I) obs: 0.356 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7

-
Processing

Software

Name	Version	Classification
PHENIX	1.8.4_1496	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3DWA

3dwa

Resolution: 2.35→40.312 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.35 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.255	1935	4.99 %	Random selection
R_work	0.192	-	-	-
obs	0.1951	38796	99.88 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.35→40.312 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6380	0	5	64	6449

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	6546
X-RAY DIFFRACTION	f_angle_d	1.372	8809
X-RAY DIFFRACTION	f_dihedral_angle_d	14.034	2372
X-RAY DIFFRACTION	f_chiral_restr	0.067	907
X-RAY DIFFRACTION	f_plane_restr	0.006	1141

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 (%)
2.35-2.4088	0.3311	133	0.3182	2629	X-RAY DIFFRACTION	100
2.4088-2.4739	0.3535	145	0.2826	2582	X-RAY DIFFRACTION	100
2.4739-2.5467	0.3181	157	0.2636	2603	X-RAY DIFFRACTION	100
2.5467-2.6289	0.3037	132	0.2527	2620	X-RAY DIFFRACTION	100
2.6289-2.7228	0.2874	146	0.2472	2603	X-RAY DIFFRACTION	100
2.7228-2.8318	0.324	146	0.2421	2615	X-RAY DIFFRACTION	100
2.8318-2.9607	0.3125	150	0.2443	2588	X-RAY DIFFRACTION	100
2.9607-3.1167	0.2968	146	0.2202	2617	X-RAY DIFFRACTION	100
3.1167-3.3119	0.2506	166	0.2114	2606	X-RAY DIFFRACTION	100
3.3119-3.5675	0.2782	110	0.184	2648	X-RAY DIFFRACTION	100
3.5675-3.9262	0.2601	113	0.174	2699	X-RAY DIFFRACTION	100
3.9262-4.4937	0.202	118	0.1484	2652	X-RAY DIFFRACTION	100
4.4937-5.6591	0.1835	133	0.1389	2666	X-RAY DIFFRACTION	100
5.6591-40.3176	0.2371	140	0.1781	2733	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	3.8259	-0.2653	-1.9336	4.0941	0.1354	4.9649	0.629	0.0844	1.1163	-0.0343	-0.0026	-0.2086	-1.0376	0.0129	-0.4582	0.5575	0.0117	0.2978	0.3423	-0.0068	0.8134	-3.7222	-34.0932	-2.5441
2	4.0412	1.6405	-3.5051	5.6782	1.5789	9.6128	-0.1583	0.52	0.673	-0.4625	0.0722	0.2982	-0.414	-0.5297	0.081	0.3438	0.0427	-0.0023	0.522	-0.0077	0.5936	-17.3807	-45.5064	-7.4719
3	4.6671	0.2259	-0.1315	5.008	0.0837	2.6475	0.8483	-0.2665	1.5378	0.0583	-0.2052	-0.1175	-1.0424	0.0778	-0.5137	0.8455	-0.0548	0.4019	0.4867	-0.0955	1.0672	-2.7709	-28.6342	1.925
4	4.2176	1.2489	-1.8297	2.5414	-1.0095	4.3903	0.6077	-0.0922	1.2637	0.1365	-0.0671	0.2755	-1.0644	-0.3442	-0.1428	0.7379	0.2455	0.4231	0.0956	-0.0734	0.8007	-6.7029	-29.9983	-0.2282
5	4.634	-0.1342	-2.5556	8.9555	2.0029	9.2021	0.1528	0.4352	-0.0767	-0.775	-0.0024	-0.2542	-0.287	-0.3357	-0.1439	0.2156	0.044	0.0673	0.3712	-0.0019	0.4119	-4.8394	-45.8879	-4.0166
6	8.1137	-1.0832	-0.296	0.3295	-0.6112	0.3534	0.1835	0.1495	0.6343	-0.2304	-0.0782	0.6406	0.1053	0.1538	-0.1575	0.5925	-0.0915	0.0944	0.5457	-0.1005	0.9736	11.4446	-38.5383	-3.1586
7	1.5847	-1.9709	1.7576	7.7455	2.4545	6.6844	-0.211	-0.3002	0.3042	0.1114	0.1357	0.3712	0.081	0.1106	0.1183	0.223	0.056	0.0304	0.3504	-0.0177	0.463	-9.7884	-54.9663	-0.208
8	6.0124	-3.1861	5.7502	9.873	-2.5855	5.6548	0.3607	-2.5972	-0.0375	1.6172	1.4144	0.3908	-0.2578	-1.9038	-0.5469	0.6541	-0.0859	0.0662	1.0218	-0.2039	0.2709	-19.6666	-44.9927	26.126
9	7.1796	-3.3485	-0.4914	7.6132	1.8595	0.9827	-0.099	-1.1856	-0.0365	1.6151	-0.3061	-1.2796	-0.1286	0.4349	0.4788	0.4199	-0.0909	-0.1254	0.6317	0.0272	0.3361	-6.9354	-58.8826	20.2394
10	7.7047	-0.739	-2.0597	7.041	0.7356	6.8878	-0.3018	-1.043	-1.113	1.2559	0.3475	-1.0975	1.007	0.428	0.0715	0.5314	0.044	-0.1627	0.6833	0.1012	0.5764	-9.5205	-61.146	23.0904
11	6.122	2.8631	-2.8576	3.3877	0.6823	3.2881	0.8431	-0.401	0.7878	0.9944	-0.4598	-0.1794	-1.605	2.1044	-0.1358	0.9344	-0.2509	-0.0482	0.9672	-0.1948	0.7713	-6.828	-40.0131	23.3789
12	3.4163	-2.0057	1.2422	2.548	-0.3233	8.0119	0.0281	-0.6928	-0.4651	1.0549	0.226	1.0855	0.6683	-0.5119	-0.1932	0.5436	0.0145	-0.0489	0.8064	0.1906	0.5984	-16.443	-63.5847	24.3288
13	5.3216	-1.5998	-0.0398	6.0795	-6.6223	9.3336	0.116	-0.6012	-0.5196	-0.9202	-0.0538	-0.1702	0.8249	-0.1241	-0.2065	0.3167	0.0164	-0.023	0.4128	-0.0427	0.3058	-14.8775	-55.1799	12.8944
14	6.9216	-0.8569	-2.2017	6.2341	-2.6322	9.2683	0.0153	-1.2751	0.4911	0.9588	-0.294	0.1234	-0.7068	0.2144	0.4748	0.3983	-0.0804	-0.0024	0.7105	-0.1149	0.3736	-16.9546	-46.9491	22.2427
15	6.9217	1.8778	-4.7703	3.9798	-0.3258	3.5496	2.1026	-6.4255	-1.2839	4.6478	2.7255	-1.3534	0.2103	2.497	-3.8152	1.9004	0.4022	-0.1006	2.1158	0.0969	1.6431	-9.661	-60.2932	33.4835
16	0.8037	-1.507	0.8021	2.8513	-1.516	0.8438	-0.3834	-1.9015	-0.3136	2.3169	1.0559	-0.8474	-0.1994	0.8871	-0.2613	1.1391	0.1609	-0.4993	1.5607	0.0407	0.9328	-4.4304	-57.4199	30.5436
17	5.5608	-0.7387	-0.0683	5.3348	-3.0867	7.1747	0.0523	-0.8374	0.6351	1.3225	0.0708	0.0023	-0.9123	-0.8283	-0.1678	0.4573	-0.0299	0.0343	0.5251	-0.1216	0.3586	-21.1319	-44.1556	19.5059
18	3.5053	-0.7393	-0.8154	1.5683	0.8315	1.8166	0.2122	-0.463	0.2866	0.1681	-0.1709	0.4977	-0.147	-0.9541	-0.1762	0.2632	-0.0408	0.0476	0.602	-0.026	0.4265	-33.8142	-49.6494	10.216
19	4.4383	1.2824	-1.8415	4.7461	-4.6571	5.4891	0.2235	-1.4185	0.1529	0.3231	0.0613	0.2987	0.2781	-0.3213	-0.3241	0.3879	-0.0273	0.0067	0.7677	0.0202	0.2998	-29.5694	-53.4719	17.928
20	4.0671	-0.4201	0.5313	6.4163	-2.5938	4.3237	-0.0877	-0.5154	0.8051	-0.0472	0.1202	0.4983	-0.3388	-0.9725	0.1261	0.3706	0.115	0.0708	0.7516	-0.092	0.4364	-33.4949	-43.9944	11.0781
21	9.2029	7.6871	-2.9786	7.0786	-4.5898	9.4189	-1.6374	-0.754	-1.3311	-0.7722	0.9685	-1.1934	-0.2361	-0.3473	0.6398	0.8557	0.1181	-0.0201	0.833	-0.0778	0.5929	-31.9842	-66.4019	16.5947
22	7.4268	5.7868	-4.877	8.404	-5.6112	4.6602	0.0705	-0.0988	-0.3594	-0.1501	-0.2714	-0.2113	0.2877	-0.0241	0.2654	0.2774	0.0098	0.0089	0.4398	-0.0489	0.2791	-25.4209	-54.3756	5.7465
23	6.564	5.111	-6.6617	4.2297	-4.6369	7.0931	0.1617	0.1799	-0.0768	0.0558	-0.2826	0.4071	-0.6251	-1.246	0.109	0.2783	-0.0534	0.0717	0.7088	-0.1338	0.5137	-36.5221	-48.7514	4.1783
24	3.7371	2.0672	-3.9967	1.8748	-3.35	5.9204	-0.5383	-1.861	1.9444	2.5023	2.4026	0.1245	0.8686	-0.2726	-1.3729	1.3	0.0253	-0.1131	1.5937	-0.2939	0.9384	-37.2866	-51.2902	23.7828
25	7.0232	0.2133	-3.1231	7.6198	-0.827	2.1529	-0.0303	-0.0893	0.2359	0.1541	0.2489	-0.0924	0.0408	-0.8802	-0.083	0.2415	0.0294	-0.0092	0.6133	-0.1259	0.4101	-36.6025	-49.0964	4.1779
26	6.4533	-3.3057	3.5969	3.1756	1.3019	8.2121	0.1239	0.8945	-1.4379	-0.6204	-0.2791	0.2637	0.6639	-1.1389	0.0515	0.3921	-0.1647	-0.0555	0.6736	-0.1786	0.5789	-30.2915	-70.8267	-16.9109
27	7.3263	2.2383	-6.178	3.1615	-1.5706	4.8798	-0.0294	0.2454	0.3076	-0.0801	0.3335	0.2566	0.3028	-0.5162	-0.335	0.2479	-0.0673	-0.0967	0.5377	-0.0152	0.3059	-35.816	-60.8109	-1.529
28	6.2723	1.3411	-4.2255	3.4192	-0.4634	6.9081	-0.029	0.4936	-0.2031	-0.3158	-0.204	-0.1367	0.0286	-0.1559	0.3961	0.3492	-0.0485	0.0304	0.6947	-0.0931	0.6912	-34.1915	-64.6357	-7.1018
29	4.4782	1.8181	-0.7404	7.3389	-0.6751	4.992	0.076	-0.1157	-0.4551	0.1936	0.0323	-0.1851	0.0325	-0.3196	-0.0601	0.1512	0.0097	0.0107	0.4555	-0.0431	0.2856	-25.9336	-64.026	-7.7585
30	7.0297	-0.4497	-4.2762	5.1631	1.3939	6.8237	-0.1742	1.0817	0.3082	-0.0876	0.2024	-0.0522	0.2054	-0.7654	0.0494	0.3786	-0.0753	-0.1138	0.596	0.0258	0.4202	-33.1208	-66.8062	-10.8881
31	3.6768	0.1187	0.2775	3.5799	-1.0427	4.2353	0.1758	0.8199	-1.4412	-0.4778	0.0575	-0.7836	0.5191	0.0285	-0.162	0.3777	-0.0499	-0.049	0.3751	-0.2248	0.8139	-11.1158	-75.9747	-8.3343
32	7.0389	-0.0919	-3.6086	5.0546	-1.5289	9.1156	0.2653	0.096	0.4914	0.1476	0.4737	0.6247	0.346	-0.6911	-0.682	0.2878	-0.0535	-0.1463	0.3642	-0.0548	0.5712	-20.5187	-76.619	-6.66
33	1.994	4.9693	-1.8377	5.8077	-4.9929	7.8566	0.61	1.2509	0.5239	-2.2371	-0.3382	1.229	-0.7025	1.6659	-0.2513	0.7753	-0.137	0.1662	1.168	-0.4289	1.1238	-4.7819	-72.4451	-18.9835
34	9.3408	2.0166	0.2995	8.4476	-0.4411	3.4252	0.1518	-0.34	-1.2282	0.3107	0.1656	0.0971	0.509	-0.3809	-0.2672	0.2968	-0.0063	-0.0503	0.3708	-0.0086	0.5884	-15.7107	-73.3762	-1.2061
35	7.3797	1.5347	0.562	2.5012	-0.706	3.5347	0.0367	0.9571	-1.2852	0.2111	0.4052	0.697	0.7695	0.1038	-0.4362	0.5527	0.0314	0.0515	0.4875	-0.1327	1.3855	-9.2381	-79.1847	-8.0072
36	8.6542	3.7175	-4.8932	3.9226	-0.0999	4.5568	-0.295	2.7637	-1.1212	-0.2384	-1.2364	0.3472	-0.8041	-0.9864	1.2367	0.9331	-0.0251	-0.0129	1.086	-0.4205	1.1666	-20.1126	-82.3933	-14.4944
37	5.2168	-2.1508	-2.0627	4.8877	0.7004	3.2073	-0.2221	0.3538	-1.7416	-0.1183	0.1963	-2.3136	0.3833	0.6819	0.0826	0.4645	0.1124	-0.0058	0.6238	-0.0907	1.1791	-0.0084	-73.4198	-4.6013
38	2.471	2.0087	1.9528	2.8614	4.0229	5.46	0.5194	-0.2628	-0.9389	0.7535	0.0754	-1.0232	1.0143	0.7212	-0.4054	0.492	0.106	-0.2286	0.6323	0.1681	0.9839	1.2062	-68.6992	11.5389
39	0.874	-1.8065	-0.4415	5.0772	-0.7055	3.8662	0.5618	-0.5454	-0.9117	0.1966	-0.5157	-0.4055	0.3214	0.2449	-0.0588	0.3796	0.0559	-0.1321	0.5095	0.0434	0.9773	1.9252	-71.1138	8.8645
40	5.1144	3.8084	5.571	4.4135	6.1533	8.5974	0.6764	-0.3039	-0.7762	2.4765	-0.7082	0.3601	2.1331	-0.2275	-0.0746	1.1443	-0.1748	-0.1214	0.8199	0.1559	1.02	-13.3896	-77.8542	16.266
41	0.3458	-0.5801	0.2932	6.5176	-2.3589	7.775	-0.0132	-0.2083	-0.9509	-0.047	-0.2913	-0.0014	0.2191	-0.0218	0.1447	0.2516	0.0007	-0.0447	0.3695	0.0108	0.5207	-7.2365	-63.2351	8.156
42	6.5139	0.1899	-0.9351	4.1432	0.6872	7.3144	-0.1635	-0.7003	-0.8694	0.9921	0.1105	-1.1395	-0.1304	0.4415	0.0052	0.273	-0.0387	-0.0739	0.5791	0.1123	0.6493	2.9643	-63.528	15.567
43	0.0484	0.0801	0.2811	0.06	0.1764	1.151	-0.4772	-1.1467	-1.5242	-0.6755	-1.3724	-1.0977	-1.2983	-0.9275	1.5942	1.0569	0.3984	-0.3141	1.4864	0.3233	1.7585	1.6688	-82.0613	13.694
44	6.738	-4.3342	-5.1	4.7027	4.3933	4.5809	1.4354	2.0523	-1.5179	-0.29	-0.5336	-0.6497	0.2868	-0.3597	-1.0877	0.9096	0.2935	-0.1316	0.9497	0.0268	1.2238	4.6433	-80.6006	7.3463
45	5.2226	-4.7318	1.1298	7.4776	-4.3213	9.1224	-0.0732	-0.9478	-0.1239	1.2132	0.2604	-0.8626	-0.745	0.4415	-0.1711	0.3423	-0.0298	-0.0805	0.7234	0.0574	0.6376	1.9968	-58.6495	17.9848

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 99 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 100 through 116 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 117 through 139 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 140 through 177 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 178 through 197 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 198 through 213 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 214 through 226 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 0 through 9 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 10 through 21 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 22 through 34 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 35 through 43 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 44 through 57 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 58 through 71 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 72 through 81 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 82 through 87 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 88 through 95 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 96 through 114 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 0 through 21 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 22 through 34 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 35 through 50 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 51 through 57 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 58 through 71 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 72 through 81 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 82 through 89 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 90 through 114 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 0 through 9 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 10 through 34 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 35 through 57 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 58 through 81 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 82 through 114 )
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 0 through 21 )
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 22 through 34 )
33	X-RAY DIFFRACTION	33	chain 'E' and (resid 35 through 43 )
34	X-RAY DIFFRACTION	34	chain 'E' and (resid 44 through 71 )
35	X-RAY DIFFRACTION	35	chain 'E' and (resid 72 through 86 )
36	X-RAY DIFFRACTION	36	chain 'E' and (resid 87 through 95 )
37	X-RAY DIFFRACTION	37	chain 'E' and (resid 96 through 114 )
38	X-RAY DIFFRACTION	38	chain 'F' and (resid 0 through 21 )
39	X-RAY DIFFRACTION	39	chain 'F' and (resid 22 through 50 )
40	X-RAY DIFFRACTION	40	chain 'F' and (resid 51 through 57 )
41	X-RAY DIFFRACTION	41	chain 'F' and (resid 58 through 71 )
42	X-RAY DIFFRACTION	42	chain 'F' and (resid 72 through 81 )
43	X-RAY DIFFRACTION	43	chain 'F' and (resid 82 through 86 )
44	X-RAY DIFFRACTION	44	chain 'F' and (resid 87 through 95 )
45	X-RAY DIFFRACTION	45	chain 'F' and (resid 96 through 114 )

-
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