PDB-7yrt: Crystal structure of PAS like domain of FlrB, the histidine kinas...

ID or keywords:

Entry

Database: PDB / ID: 7yrt

Title

Crystal structure of PAS like domain of FlrB, the histidine kinase involved in flagellar synthesis of Vibrio cholerae

Components

histidine kinase

Keywords

SIGNALING PROTEIN / Vibrio cholerae / Flagellar gene transcription / Sensor histidine kinase / PAS like domain / Phosphorylation

Function / homology

Function and homology information

histidine kinase / phosphorelay sensor kinase activity
Similarity search - Function

Biological species

Vibrio cholerae O395 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.27 Å

Authors

Dasgupta, J. / Mukherjee, P.

Funding support

India, 1items

Citation

Journal: Structure / Year: 2024
Title: PAS domain of flagellar histidine kinase FlrB has a unique architecture and binds heme as a sensory ligand in an unconventional fashion.
Authors: Mukherjee, P. / Agarwal, S. / Mallick, S.B. / Dasgupta, J.

History

Deposition	Aug 10, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 5, 2022	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0	May 1, 2024	Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7yrt.cif.gz	565.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7yrt.ent.gz	469.2 KB	Display	PDB format
PDBx/mmJSON format	7yrt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7yrt_validation.pdf.gz	535.2 KB	Display	wwPDB validaton report
Full document	7yrt_full_validation.pdf.gz	551.1 KB	Display
Data in XML	7yrt_validation.xml.gz	46.8 KB	Display
Data in CIF	7yrt_validation.cif.gz	64 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yr/7yrt ftp://data.pdbj.org/pub/pdb/validation_reports/yr/7yrt	HTTPS FTP

-
Related structure data

Similar structure data	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	#190 - Oct 2015 Two-component Systems similarity (8) #183 - Mar 2015 Phototropin similarity (8)

Deposited unit

A: histidine kinase

B: histidine kinase

C: histidine kinase

D: histidine kinase

E: histidine kinase

F: histidine kinase

G: histidine kinase

H: histidine kinase

I: histidine kinase

J: histidine kinase

K: histidine kinase

L: histidine kinase

187 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: histidine kinase

E: histidine kinase

defined by author&software
Evidence: cross-linking
31.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: histidine kinase

F: histidine kinase

defined by author&software
31.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: histidine kinase

K: histidine kinase

defined by author&software
31.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: histidine kinase

L: histidine kinase

defined by author&software
31.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

G: histidine kinase

I: histidine kinase

defined by author&software
31.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

H: histidine kinase

J: histidine kinase

defined by author&software
31.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	212.644, 49.556, 146.830
Angle α, β, γ (deg.)	90.00, 92.53, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	histidine kinase Mass: 15544.545 Da / Num. of mol.: 12 / Fragment: PAS domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O395 (bacteria) / Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: flrB, VC0395_A1720 / Plasmid: pET28a+ / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0H3AMQ9, histidine kinase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

histidine kinase

Mass: 15544.545 Da / Num. of mol.: 12 / Fragment: PAS domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vibrio cholerae O395 (bacteria) / Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: flrB, VC0395_A1720 / Plasmid: pET28a+ / Production host:

Escherichia coli BL21 (bacteria) / References: UniProt: A0A0H3AMQ9, histidine kinase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.48 Å³/Da / Density % sol: 50.39 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.8 M Ammonium sulfate, 0.1 M Citric Acid pH 5, 10% Glycerol

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972423 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 4, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.972423 Å / Relative weight: 1
Reflection	Resolution: 2.27→48.26 Å / Num. obs: 69328 / % possible obs: 97.7 % / Redundancy: 2.6 % / CC_1/2: 0.997 / R_merge(I) obs: 0.046 / Net I/σ(I): 9.1
Reflection shell	Resolution: 2.27→2.35 Å / Num. unique obs: 6819 / CC_1/2: 0.526

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Alphafold2

Resolution: 2.27→48.26 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2507	3383	4.89 %
R_work	0.1849	-	-
obs	0.1883	69160	96.68 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.27→48.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10946	0	0	85	11031

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11076
X-RAY DIFFRACTION	f_angle_d	1.062	15011
X-RAY DIFFRACTION	f_dihedral_angle_d	15.677	4249
X-RAY DIFFRACTION	f_chiral_restr	0.04	1796
X-RAY DIFFRACTION	f_plane_restr	0.006	1961

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 (%)
2.27-2.3024	0.4395	112	0.3666	2688	X-RAY DIFFRACTION	96
2.3024-2.3368	0.4342	147	0.351	2747	X-RAY DIFFRACTION	98
2.3368-2.3733	0.4338	131	0.3242	2801	X-RAY DIFFRACTION	98
2.3733-2.4122	0.4065	136	0.3136	2678	X-RAY DIFFRACTION	98
2.4122-2.4538	0.3484	109	0.3113	2834	X-RAY DIFFRACTION	98
2.4538-2.4984	0.3759	112	0.2949	2797	X-RAY DIFFRACTION	98
2.4984-2.5465	0.3479	121	0.2781	2738	X-RAY DIFFRACTION	97
2.5465-2.5985	0.3159	127	0.2826	2726	X-RAY DIFFRACTION	95
2.5985-2.655	0.3434	154	0.2656	2671	X-RAY DIFFRACTION	97
2.655-2.7167	0.3038	153	0.2654	2797	X-RAY DIFFRACTION	99
2.7167-2.7847	0.326	157	0.2625	2729	X-RAY DIFFRACTION	98
2.7847-2.8599	0.3791	155	0.2706	2764	X-RAY DIFFRACTION	98
2.8599-2.9441	0.36	154	0.2668	2776	X-RAY DIFFRACTION	98
2.9441-3.0391	0.3542	149	0.2539	2732	X-RAY DIFFRACTION	98
3.0391-3.1477	0.3058	151	0.2453	2733	X-RAY DIFFRACTION	98
3.1477-3.2737	0.3053	167	0.2269	2768	X-RAY DIFFRACTION	98
3.2737-3.4227	0.2832	153	0.2111	2719	X-RAY DIFFRACTION	96
3.4227-3.603	0.2535	128	0.1986	2753	X-RAY DIFFRACTION	96
3.603-3.8287	0.2574	137	0.1693	2681	X-RAY DIFFRACTION	94
3.8287-4.1242	0.2194	153	0.1466	2743	X-RAY DIFFRACTION	96
4.1242-4.5389	0.1905	123	0.1255	2768	X-RAY DIFFRACTION	96
4.5389-5.1951	0.1653	130	0.1245	2734	X-RAY DIFFRACTION	95
5.1951-6.5426	0.2143	163	0.1533	2721	X-RAY DIFFRACTION	95
6.5426-48.26	0.1672	161	0.1089	2679	X-RAY DIFFRACTION	90

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	3.3027	3.2539	1.2491	3.1978	1.2807	9.9757	-0.4899	0.1984	1.7705	-1.3364	1.1941	1.3394	-0.8981	-0.6747	-0.2791	0.8071	-0.0251	-0.1804	0.5734	0.1873	1.3569	-13.9419	16.0117	51.052
2	3.6477	1.3653	3.7648	9.9088	-1.3248	5.953	-0.246	-0.4036	0.2374	0.1621	0.4362	0.7832	-0.0539	-0.7515	-0.2371	0.3669	-0.0383	0.0621	0.4891	-0.067	0.6096	-3.5919	7.8836	59.0589
3	4.1947	-4.0594	0.7335	4.9584	-2.199	8.5531	-0.7695	-1.2534	1.631	0.4722	0.8641	-0.7171	-0.731	0.4897	0.0211	0.3908	0.0451	-0.0946	0.5385	-0.2375	0.6224	8.4782	9.6221	68.0138
4	9.5236	-5.5145	0.1947	6.4021	-2.5877	5.7393	0.1957	-1.3216	-0.5268	0.0683	0.1472	0.3703	0.512	-0.7659	-0.4025	0.5205	-0.148	-0.0227	0.6244	0.0729	0.4887	1.9314	-4.2537	66.5207
5	6.7946	-2.1101	1.1547	2.6221	-0.3882	6.6049	0.3782	-1.1098	-0.0318	0.1859	-0.0179	-0.3149	0.124	-0.2554	-0.1278	0.5056	-0.0401	-0.0348	0.6248	-0.0314	0.5058	11.8621	0.811	72.2604
6	6.169	-6.0605	-6.0531	5.906	5.9201	5.9381	-0.2316	0.1107	-0.3163	0.483	0.688	-0.0163	0.8649	0.6472	-0.2654	0.7263	-0.0553	-0.1795	0.5364	-0.0013	0.945	18.0752	-12.5833	65.0452
7	2.989	-2.6605	1.5641	7.6442	-2.4626	5.6286	0.2937	-0.0522	-0.0972	-0.3845	0.1638	0.7834	0.6242	-0.1498	-0.452	0.4113	-0.0771	-0.0175	0.3782	0.0268	0.5258	11.9343	-4.4768	61.1783
8	1.5193	-2.7797	0.9402	8.8909	-1.2628	5.5715	0.3038	-0.2781	-0.3897	-0.4406	0.0044	0.8737	0.2111	-0.3251	-0.4687	0.3543	-0.0664	-0.0037	0.4837	0.0641	0.6947	8.7107	-0.4941	59.3188
9	5.5299	-4.5061	-2.8916	9.8355	6.4562	4.1953	-0.4097	-0.0436	-0.6695	0.5427	0.2913	-0.0761	0.9235	0.2592	0.1855	0.7133	-0.0442	-0.021	0.488	0.0548	0.8243	10.2977	-23.837	54.093
10	7.6896	-2.1574	-3.021	2.5949	-0.8523	2.6907	0.3794	-0.8172	0.6203	1.0807	-0.3124	-1.1198	-0.6663	0.9536	-0.0107	0.6948	0.0224	-0.092	0.7993	-0.0503	0.9177	10.4659	34.263	21.8943
11	7.295	-1.8987	2.8281	6.963	-0.6347	4.6326	-0.2334	-0.147	-0.0875	0.0049	0.2107	-0.6122	0.185	0.5229	-0.0636	0.4535	0.0451	0.1	0.5378	0.0293	0.5186	-0.6442	26.7268	13.3558
12	4.9124	-0.7602	-2.7605	5.9211	4.9421	6.4672	-0.4817	0.3612	-0.1645	0.2863	0.7444	-0.1512	0.0964	0.6156	-0.2419	0.3979	0.0221	0.1049	0.6129	0.0324	0.4816	-8.8242	21.8184	5.3108
13	2.8237	2.6022	1.4923	3.9749	-2.0406	7.829	0.4844	1.3507	0.482	-0.2716	0.0688	-0.0786	-0.093	0.3703	-0.3528	0.442	0.0252	0.1046	0.5391	-0.0477	0.5593	-15.4734	19.6168	0.6084
14	8.2105	0.75	1.0446	5.0727	-4.9345	5.0817	-0.0904	-0.1415	-0.9107	0.0991	0.6449	1.3662	0.7991	-0.5827	-0.4361	0.5835	0.0062	0.0928	0.5079	-0.0206	0.8582	-21.2376	6.9751	10.5662
15	5.9725	0.5747	-0.2457	3.3407	4.5246	6.2669	-0.1522	0.2577	-0.1699	-0.1051	0.0824	-0.5909	0.5337	0.1819	0.0723	0.5484	0.046	0.0786	0.3707	0.1222	0.4067	-14.8127	15.2141	10.7464
16	-0.0878	0.5438	-0.4476	6.619	-2.3272	2.2704	0.0651	0.0511	-0.1757	-0.2603	-0.188	0.5416	0.5278	0.0775	0.0342	0.7033	0.1354	0.0689	0.4077	0.0448	0.8648	-13.4546	2.584	16.7918
17	5.6778	-1.0426	-1.1601	2.0796	0.0162	2.3074	0.0426	-0.0295	0.0959	-0.1639	0.0008	-0.0183	-0.0562	-0.0047	-0.0825	0.4388	-0.0604	-0.0234	0.3587	-0.0064	0.3325	-42.059	2.1011	57.6349
18	2.4271	-3.4585	3.8278	5.9024	-6.394	7.3946	0.4599	0.1617	0.4668	-0.3686	-0.2032	0.1224	-0.6219	-0.5698	-0.3323	0.7374	0.0012	0.081	0.7494	0.052	0.6762	-47.2175	15.7217	33.5736
19	6.6807	3.9833	-0.6649	5.291	-0.8889	2.5855	-0.2586	0.625	0.0433	0.072	0.3516	0.3171	-0.0484	-0.302	-0.1342	0.4269	0.1101	-0.0489	0.5518	0.0124	0.4705	-71.3179	-5.6955	11.765
20	4.3214	2.2937	4.6601	3.1002	3.5479	5.6262	1.2136	-0.5309	0.2081	0.7309	-0.1227	-0.5127	1.1769	-1.0041	-1.271	0.6674	-0.0029	-0.203	0.8797	0.0047	0.6684	-53.6573	8.9721	22.8972
21	3.7935	0.5752	-0.9854	8.123	1.9056	3.6343	0.0287	-0.6406	-0.3011	0.9982	-0.0783	-0.2439	0.2758	0.4926	0.0372	0.6018	0.1253	-0.0831	0.6238	0.0562	0.5049	-61.1558	0.5014	21.9336
22	2.9359	4.4645	3.5683	8.3229	6.0021	4.4734	-0.4671	0.1767	1.083	1.3567	0.6425	-0.2302	-1.379	0.6837	-0.5334	1.315	0.0198	-0.1223	0.8744	-0.0712	1.1341	-66.8512	13.3964	37.5954
23	7.6145	-2.9091	0.1709	5.9869	0.8132	6.6207	-0.3227	-0.7975	1.274	0.0255	0.3157	-0.1198	-0.6866	0.4879	0.2494	0.3957	-0.0344	-0.031	0.4606	-0.0601	0.7375	5.0281	15.413	60.315
24	2.3312	2.1748	1.7372	4.7312	1.1111	3.721	0.0987	1.6475	0.6176	-0.6522	0.0031	-0.1502	-0.0767	0.2902	-0.1452	0.4209	0.0041	0.0249	0.7258	0.1083	0.499	-8.1824	3.631	42.7402
25	2.3534	-1.6132	3.8595	2.1353	-1.0716	8.9212	0.7779	0.9211	-1.8242	-0.788	-0.7143	0.6244	1.5862	-0.1758	-0.3637	0.7294	0.0376	-0.1321	0.8811	-0.2577	1.0612	-9.6856	-14.5798	42.424
26	9.0708	-5.8679	-1.2571	4.3948	2.7061	5.1518	0.3179	0.514	-0.2592	-0.5634	-0.2735	0.004	-0.0464	0.1537	-0.119	0.4655	-0.0197	0.0459	0.6461	-0.0118	0.5631	-7.5774	-4.2242	47.4506
27	4.9748	-4.9784	-0.4855	4.9965	-0.1091	5.59	0.4714	-0.0949	-1.2614	-0.6935	-0.8431	0.3174	1.0788	-0.2989	0.4708	0.7824	-0.0489	0.0338	0.6757	-0.0193	0.8744	3.0741	-23.6285	47.0009
28	2.326	3.5211	-0.651	6.523	-0.0536	4.4871	-0.4851	0.1853	1.258	0.033	0.7534	0.5939	-0.5404	-0.5486	-0.1385	0.4972	0.0019	0.0343	0.5722	0.0612	0.7857	-7.8574	33.7283	12.9646
29	5.9312	0.6957	0.7538	4.7156	-1.3283	3.0674	-0.0471	-1.0782	-0.1099	0.5893	0.0548	-0.0616	0.0498	-0.2577	-0.0289	0.4831	0.0812	0.0432	0.9528	0.0781	0.5112	4.8641	19.6492	30.2811
30	6.5901	7.1031	-6.0037	8.6229	-4.3419	9.5397	0.3379	-0.6994	-0.3315	0.2551	-0.7325	-0.3411	0.2385	0.6623	0.3729	0.3898	0.0885	0.0385	0.8217	0.1982	0.5537	4.4007	12.0727	25.082
31	2.7679	5.1119	1.2819	10.008	3.4591	2.1209	-0.295	0.0352	-1.581	1.5621	-0.2433	-0.2767	1.4843	0.1639	0.5066	1.0984	0.16	0.1773	0.7624	-0.0064	0.9528	-6.9019	-6.11	25.6163
32	2.0043	2.0422	-1.5394	3.3014	-0.6781	4.1715	-0.0184	0.2496	-0.2568	-0.3153	-0.0727	-0.1812	0.3178	0.5238	0.121	0.4392	0.0738	-0.0708	0.5433	-0.0152	0.5096	-70.1864	-17.1004	54.9827
33	9.0119	1.2601	1.058	5.3524	-0.0501	5.3731	0.5065	-0.3675	-0.3694	0.1279	-0.1807	0.1511	1.0236	-0.2469	-0.3887	0.4762	-0.0372	-0.0913	0.3609	-0.0017	0.5067	-81.1816	-26.4291	69.54
34	2.9632	-0.3217	2.1629	3.5187	-0.4786	5.5385	-0.078	0.136	0.1794	0.1105	-0.2576	0.058	-0.2657	-0.2018	0.326	0.3652	-0.0073	-0.0311	0.4833	-0.0209	0.4537	-80.8862	-15.9999	68.8335
35	5.7448	1.4106	3.4669	9.5088	5.2207	4.0575	0.0607	-1.1757	0.0651	1.8166	-0.0717	0.1417	-0.3455	-0.5216	0.0441	0.9441	0.0279	0.0518	0.6107	-0.0024	0.6456	-77.2405	-4.9483	86.7325
36	7.7784	3.2981	-1.4162	2.566	0.225	0.8587	0.8933	-0.9771	-0.5056	1.4426	-0.2155	0.5293	0.1773	-1.7137	-0.5537	0.8637	0.1084	0.0771	1.2757	0.1581	0.6927	-47.9378	37.2028	31.3392
37	2.8816	-3.9741	0.6393	6.7421	0.63	2.1574	-0.2531	-0.477	-0.3586	0.3793	0.3327	0.4388	0.1566	-0.4192	-0.0084	0.488	-0.0109	0.0009	0.7446	0.0912	0.5392	-40.673	29.4509	19.8854
38	5.5005	-4.9041	5.1098	9.8328	-5.4627	4.9321	-0.2436	-1.3224	-1.0354	0.6263	0.1942	0.1365	-0.5179	0.1472	-0.0312	0.677	-0.0313	0.0226	0.698	0.0558	0.4516	-30.5063	18.2927	16.9854
39	3.9331	-5.2073	-4.1639	7.2623	5.5199	4.3897	0.3384	-0.8164	-1.6641	-0.5172	-0.5372	0.1384	0.0657	-0.9567	0.2234	0.4292	-0.0269	-0.126	0.5867	0.0659	0.7732	-39.2603	24.286	5.6357
40	7.7594	-1.1725	0.6393	9.1149	4.5572	7.6684	0.5786	-0.4082	-0.8785	0.1882	-0.1568	0.5895	1.0346	-0.2314	-0.3049	0.4573	-0.0694	-0.0312	0.3872	0.0838	0.5193	-29.9406	15.9158	6.8056
41	8.2608	1.1247	-4.5144	2.1544	-1.3466	6.517	0.1009	0.8167	0.1811	-1.0867	-0.3578	-1.4156	-0.2968	0.8624	0.2451	0.6996	-0.0234	0.214	0.738	0.0792	0.8173	-24.439	27.5806	-4.2344
42	5.5819	-1.8922	4.2039	5.1395	0.8879	3.6537	-0.0511	-0.1429	0.3503	-0.08	-0.051	-0.1722	-0.1228	-0.5333	0.183	0.3943	-0.0816	0.0386	0.4632	0.0859	0.4329	-29.6732	27.4343	6.2568
43	8.5572	-3.717	3.0573	5.9851	-0.098	7.2874	-0.1078	1.4414	0.5681	-1.8949	0.1153	-0.6915	-0.644	0.8709	-0.085	0.9993	-0.1996	0.0126	0.7275	0.0442	0.7433	-32.0853	39.4496	-13.0579
44	6.0276	4.0123	-2.43	7.3337	0.4389	7.6964	-0.3709	0.9204	-0.3519	-1.1958	0.0424	0.5281	0.6718	-0.3515	0.2916	0.5188	-0.0352	-0.124	0.6667	-0.0379	0.5025	-77.0242	-17.9423	49.1894
45	4.3958	2.994	0.5784	8.1942	0.1407	2.373	-0.138	0.6515	0.5839	-0.3482	0.1024	0.5454	-0.2766	-0.0127	-0.0067	0.3764	0.0708	-0.0289	0.5366	0.1077	0.443	-66.6874	2.1484	54.2907
46	3.3649	-4.0127	3.3439	9.9745	-4.0627	3.5486	0.3396	-0.2304	-0.4481	0.7773	0.5747	0.4102	-0.9367	0.3078	-0.9086	0.6828	0.013	0.0641	0.6099	-0.0381	0.6186	-63.8797	6.7382	69.5031
47	5.3836	-4.3068	-5.2221	7.3168	3.8229	4.9685	0.1729	0.2694	-0.355	-0.1785	-0.1478	0.3015	-0.0691	-0.0847	-0.1733	0.429	0.0583	-0.0672	0.5666	-0.0364	0.3974	-62.9227	-5.037	60.245
48	8.5531	-2.5565	-4.1528	6.7203	1.399	2.0931	0.1249	-1.4709	0.4221	1.6103	0.0983	0.2558	-0.4139	0.1023	-0.2575	1.0477	-0.115	0.2202	0.7559	-0.1003	0.7118	-70.7582	2.1928	83.4259
49	5.2496	-0.9822	0.7734	5.6495	-0.2075	3.7783	-0.3492	-0.7795	0.1278	0.6306	0.3673	-0.4865	-0.0428	0.1835	-0.0331	0.4534	0.034	-0.0389	0.5372	-0.0144	0.5114	-40.0713	41.5515	20.6968
50	6.5924	1.6136	-2.9946	6.9748	-1.8617	2.6927	0.3654	0.0883	0.2347	-0.381	-0.0646	-0.0901	-0.6949	-0.0359	-0.2795	0.5707	-0.0341	0.023	0.6563	0.0084	0.5849	-46.6034	46.8493	7.2577
51	6.7373	2.6298	-4.9065	2.4039	-2.4291	3.3938	-0.1096	0.5958	0.4768	-0.5116	0.1312	-0.2718	-0.2267	-0.5541	-0.2792	0.6283	0.0688	0.1177	0.5087	0.0609	0.7266	-40.6423	44.4724	-2.3425
52	6.2875	0.298	-2.1006	7.115	-2.9563	2.1427	-0.139	-0.4657	-0.9079	0.5672	-0.036	0.2722	0.6231	-0.5257	0.1178	0.4554	-0.037	-0.0328	0.5669	0.076	0.8153	-41.3293	-9.2751	63.1347
53	9.8095	-0.2065	-1.7753	1.7539	-0.4659	8.2662	-0.009	0.9641	-0.7167	-0.3264	-0.0794	0.0563	0.3653	-0.0017	0.072	0.3632	0.0065	-0.0313	0.4307	-0.1312	0.5226	-25.499	-7.8771	43.3296
54	9.4364	-2.089	4.7842	8.1712	-3.5516	8.4241	0.0947	1.2812	0.6537	-0.4712	-0.348	0.1747	-0.4358	0.4653	0.153	0.3377	-0.032	-0.0257	0.6083	-0.0165	0.5913	-26.1104	1.7822	41.1285
55	7.5707	-7.4593	7.2461	9.5196	-8.2098	8.6108	-0.1211	0.4935	0.9733	-0.4793	-0.438	-0.484	0.0089	0.3177	0.7792	0.5129	-0.0744	-0.0671	0.5962	0.0794	0.6352	-35.2509	8.402	34.8745
56	7.9237	-5.1257	-2.5818	3.9645	2.7765	2.737	0.4239	0.2047	1.6094	-0.8444	-0.3935	-1.731	0.0264	1.0408	-0.2134	0.8355	0.0072	0.1288	0.733	-0.0195	1.046	-62.1753	-13.8155	2.7719
57	6.7004	0.7013	-3.1516	1.3152	0.3788	4.2979	-0.3368	-0.1418	-0.8526	0.2543	0.1495	-0.2216	0.5751	0.3423	0.1225	0.4454	0.1235	-0.0241	0.5665	0.0992	0.772	-72.6441	-13.6858	16.5723
58	6.8005	0.7301	-2.7603	2.1233	0.4402	4.1264	-0.0884	-0.9367	-1.0564	0.624	0.0271	-0.2032	0.6466	0.1241	0.2331	0.6464	0.1779	0.0369	0.8863	0.3315	0.8304	-84.7101	-16.276	28.5484
59	2.652	-0.2553	-1.6083	5.8578	3.7305	3.2896	-1.3748	-1.4761	-0.7778	1.2388	0.7958	0.2653	-0.2983	1.3416	0.2016	0.6871	0.0825	0.0615	1.392	0.2434	0.6897	-88.5017	-4.432	40.2511
60	6.1231	1.7208	-0.5385	8.7667	7.6578	7.8014	0.296	-1.0081	-0.0242	0.3297	-0.3098	-0.071	-0.2366	-0.1422	-0.0524	0.4495	0.092	-0.0242	0.932	0.1739	0.5553	-83.8727	-4.2373	31.3889
61	1.2624	0.164	0.7127	3.0662	2.2703	5.504	-0.1513	-0.5663	0.4529	0.5333	0.0098	0.0055	-0.3698	0.0292	-0.0363	0.7725	0.1364	-0.0447	0.9004	0.0817	0.744	-77.3066	3.3869	36.8175

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 15 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 16 through 37 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 38 through 47 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 48 through 54 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 55 through 70 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 71 through 77 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 78 through 98 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 99 through 107 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 108 through 123 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 9 through 15 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 16 through 38 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 39 through 54 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 55 through 70 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 71 through 80 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 81 through 98 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 99 through 123 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 6 through 107 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 108 through 123 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 6 through 70 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 71 through 75 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 76 through 107 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 108 through 122 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 7 through 29 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 30 through 70 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 71 through 80 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 81 through 107 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 108 through 122 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 8 through 29 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 30 through 75 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 76 through 107 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 108 through 123 )
32	X-RAY DIFFRACTION	32	chain 'G' and (resid 9 through 54 )
33	X-RAY DIFFRACTION	33	chain 'G' and (resid 55 through 75 )
34	X-RAY DIFFRACTION	34	chain 'G' and (resid 76 through 107 )
35	X-RAY DIFFRACTION	35	chain 'G' and (resid 108 through 123 )
36	X-RAY DIFFRACTION	36	chain 'H' and (resid 9 through 15 )
37	X-RAY DIFFRACTION	37	chain 'H' and (resid 16 through 37 )
38	X-RAY DIFFRACTION	38	chain 'H' and (resid 38 through 47 )
39	X-RAY DIFFRACTION	39	chain 'H' and (resid 48 through 54 )
40	X-RAY DIFFRACTION	40	chain 'H' and (resid 55 through 70 )
41	X-RAY DIFFRACTION	41	chain 'H' and (resid 71 through 80 )
42	X-RAY DIFFRACTION	42	chain 'H' and (resid 81 through 107 )
43	X-RAY DIFFRACTION	43	chain 'H' and (resid 108 through 123 )
44	X-RAY DIFFRACTION	44	chain 'I' and (resid 9 through 29 )
45	X-RAY DIFFRACTION	45	chain 'I' and (resid 30 through 70 )
46	X-RAY DIFFRACTION	46	chain 'I' and (resid 71 through 88 )
47	X-RAY DIFFRACTION	47	chain 'I' and (resid 89 through 107 )
48	X-RAY DIFFRACTION	48	chain 'I' and (resid 108 through 122 )
49	X-RAY DIFFRACTION	49	chain 'J' and (resid 14 through 70 )
50	X-RAY DIFFRACTION	50	chain 'J' and (resid 71 through 98 )
51	X-RAY DIFFRACTION	51	chain 'J' and (resid 99 through 122 )
52	X-RAY DIFFRACTION	52	chain 'K' and (resid 8 through 29 )
53	X-RAY DIFFRACTION	53	chain 'K' and (resid 30 through 75 )
54	X-RAY DIFFRACTION	54	chain 'K' and (resid 76 through 98 )
55	X-RAY DIFFRACTION	55	chain 'K' and (resid 99 through 123 )
56	X-RAY DIFFRACTION	56	chain 'L' and (resid 7 through 15 )
57	X-RAY DIFFRACTION	57	chain 'L' and (resid 16 through 37 )
58	X-RAY DIFFRACTION	58	chain 'L' and (resid 38 through 70 )
59	X-RAY DIFFRACTION	59	chain 'L' and (resid 71 through 75 )
60	X-RAY DIFFRACTION	60	chain 'L' and (resid 76 through 98 )
61	X-RAY DIFFRACTION	61	chain 'L' and (resid 99 through 122 )

-
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://pdbjlvh1.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