PDB-4xhf: Crystal structure of Shewanella oneidensis NqrC

ID or keywords:

Entry

Database: PDB / ID: 4xhf

Title

Crystal structure of Shewanella oneidensis NqrC

Components

Na-translocating NADH-quinone reductase subunit C NqrC

Keywords

OXIDOREDUCTASE / FMN / COVALENT FLAVINYLATION

Function / homology

Function and homology information

NADH:ubiquinone reductase (Na+-transporting) / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / FMN binding / plasma membrane
Similarity search - Function

Biological species

Shewanella oneidensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.76 Å

Authors

Tomchick, D.R. / Brautigam, C.A. / Deka, R.K. / Norgard, M.V.

Citation

Journal: Microbiologyopen / Year: 2016
Title: Molecular insights into the enzymatic diversity of flavin-trafficking protein (Ftp; formerly ApbE) in flavoprotein biogenesis in the bacterial periplasm.
Authors: Deka, R.K. / Brautigam, C.A. / Liu, W.Z. / Tomchick, D.R. / Norgard, M.V.

History

Deposition	Jan 5, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 16, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 16, 2016	Group: Database references
Revision 1.2	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4xhf.cif.gz	523 KB	Display	PDBx/mmCIF format
PDB format	pdb4xhf.ent.gz	438.5 KB	Display	PDB format
PDBx/mmJSON format	4xhf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xh/4xhf ftp://data.pdbj.org/pub/pdb/validation_reports/xh/4xhf	HTTPS FTP

-
Related structure data

Related structure data	4xgvC 4xgwC 4xgxC C: citing same article (ref.)
Similar structure data	2xmq-1 1xq0-d 3t5z-d 1cra-d 2h4n-d 6yzs-d 1bnn-d 4q6e-d 3nb5-d 5ehw-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

4xgvC

4xgwC

4xgxC

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Na-translocating NADH-quinone reductase subunit C NqrC

B: Na-translocating NADH-quinone reductase subunit C NqrC

C: Na-translocating NADH-quinone reductase subunit C NqrC

D: Na-translocating NADH-quinone reductase subunit C NqrC

hetero molecules

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

1

A: Na-translocating NADH-quinone reductase subunit C NqrC

hetero molecules

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

2

B: Na-translocating NADH-quinone reductase subunit C NqrC

hetero molecules

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

3

C: Na-translocating NADH-quinone reductase subunit C NqrC

hetero molecules

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

4

D: Na-translocating NADH-quinone reductase subunit C NqrC

hetero molecules

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

Unit cell

Length a, b, c (Å)	70.914, 93.476, 71.139
Angle α, β, γ (deg.)	90.000, 100.240, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Details

The biological unit is a monomer. There are 4 biological units in the asymmetric unit.

#1: Protein	Na-translocating NADH-quinone reductase subunit C NqrC Mass: 29046.902 Da / Num. of mol.: 4 / Fragment: Soluble fragment, UNP residues 33-264 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: nqrC, SO_0904 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8EID8, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 651 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	2	38.41
2

Crystal grow

Temperature (K)	Crystal-ID	Method	pH	Details
293	1	vapor diffusion, hanging drop	5	0.1 M MIB (malonate, imidazole and boric acid), 25% (w/v) PEG 1,500
293	2	vapor diffusion, hanging drop	9	0.1 M bicine, 0.1 M NaCl, 27% (w/v) PEG 1,500, 20% (v/v) ethylene glycol

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
3		2
4		2

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	19-ID	1	0.97918
SYNCHROTRON	APS	19-ID	2	0.97918

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2014 / Details: monochromator

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SAGITALLY FOCUSED Si(111)	SINGLE WAVELENGTH	M	x-ray	1
2	SAGITALLY FOCUSED Si(111)	MAD	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97918	1
2		1

Reflection twin

Operator: l,-k,h / Fraction: 0.38

Reflection

Resolution: 1.76→50 Å / Num. all: 89381 / Num. obs: 89381 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / R_merge(I) obs: 0.065 / R_pim(I) all: 0.036 / R_rim(I) all: 0.075 / Χ²: 0.855 / Net I/av σ(I): 15.927 / Net I/σ(I): 14.4 / Num. measured all: 370660

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.76-1.79	3.4	0.384	4319	0.748	0.241	0.456	0.664	96.3
1.79-1.82	3.6	0.343	4413	0.812	0.21	0.404	0.68	98.1
1.82-1.86	4	0.285	4446	0.895	0.162	0.328	0.734	98.4
1.86-1.9	4.2	0.229	4418	0.924	0.127	0.262	0.767	98.7
1.9-1.94	4.2	0.2	4442	0.943	0.11	0.229	0.865	98.5
1.94-1.98	4.2	0.165	4461	0.957	0.091	0.189	0.872	98.9
1.98-2.03	4.2	0.144	4447	0.964	0.08	0.165	0.873	98.9
2.03-2.09	4.2	0.133	4430	0.968	0.073	0.152	0.952	99
2.09-2.15	4.2	0.116	4466	0.976	0.064	0.133	0.917	99
2.15-2.22	4.3	0.102	4482	0.98	0.057	0.117	0.939	99.2
2.22-2.3	4.3	0.097	4496	0.982	0.053	0.111	0.977	99.2
2.3-2.39	4.3	0.089	4459	0.982	0.05	0.102	0.933	99.3
2.39-2.5	4.3	0.083	4479	0.982	0.046	0.095	0.893	99.4
2.5-2.63	4.3	0.078	4491	0.986	0.043	0.089	0.908	99.6
2.63-2.79	4.3	0.073	4474	0.987	0.041	0.084	0.903	99.6
2.79-3.01	4.3	0.069	4539	0.989	0.039	0.079	0.908	99.7
3.01-3.31	4.3	0.065	4479	0.991	0.036	0.075	0.924	99.8
3.31-3.79	4.2	0.059	4575	0.995	0.033	0.067	0.901	99.9
3.79-4.78	4.1	0.051	4534	0.996	0.029	0.059	0.76	99.9
4.78-50	4.2	0.044	4531	0.998	0.025	0.05	0.623	97.7

-
Processing

Software

Name	Version	Classification
HKL-3000		data reduction
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.76→33.713 Å / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.7 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2016	2032	2.29 %	random selection
R_work	0.1657	86864	-	-
obs	0.1684	88913	98.32 %	-

Solvent computation

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

Displacement parameters

B_iso max: 83.5 Å² / B_iso mean: 23.853 Å² / B_iso min: 6.06 Å²

Refinement step

Cycle: final / Resolution: 1.76→33.713 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6917	0	197	651	7765
B_iso mean	-	-	27.8	22.46	-
Num. residues	-	-	-	-	884

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	7243
X-RAY DIFFRACTION	f_angle_d	0.648	9785
X-RAY DIFFRACTION	f_chiral_restr	0.026	1043
X-RAY DIFFRACTION	f_plane_restr	0.002	1249
X-RAY DIFFRACTION	f_dihedral_angle_d	12.031	2661

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7606-1.8046	0.2482	132	0.2351	5722	5854	89
1.8046-1.8533	0.2603	141	0.2252	6128	6269	96
1.8533-1.9078	0.2335	139	0.2101	6200	6339	96
1.9078-1.9694	0.2474	140	0.2017	6212	6352	96
1.9694-2.0397	0.2411	147	0.1917	6201	6348	97
2.0397-2.1213	0.2221	142	0.1871	6203	6345	97
2.1213-2.2178	0.2285	147	0.1789	6255	6402	97
2.2178-2.3346	0.1948	141	0.1767	6222	6363	97
2.3346-2.4807	0.1653	143	0.1756	6219	6362	97
2.4807-2.6719	0.2141	146	0.1713	6307	6453	97
2.6719-2.9403	0.1954	144	0.1707	6295	6439	97
2.9403-3.3645	0.2038	144	0.1553	6293	6437	98
3.3645-4.234	0.1791	147	0.1329	6317	6464	98
4.234-22.1683	0.184	152	0.144	6290	6442	96

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	3.6353	2.1691	-1.2659	1.9106	-1.0666	1.5857	0.0768	0.0393	-0.3397	0.057	-0.0075	0.124	0.3422	-0.1038	-0.0045	0.2148	-0.0105	-0.0218	0.0939	0.0246	0.2015	-1.6243	-5.6578	45.9358
2	2.2923	-0.8615	0.0009	1.4643	0.3242	1.1975	-0.1895	-0.2682	0.0541	0.1714	0.1474	-0.1118	0.1291	0.0811	0.039	0.1139	0.0302	0.0077	0.1316	0.0028	0.1104	5.9819	3.3942	47.2614
3	1.0965	0.175	0.4221	0.9965	-0.2282	1.6919	0.0237	-0.0753	0.0156	0.1701	0.0724	0.2733	-0.0105	-0.2794	-0.0417	0.193	-0.0032	0.0144	0.1595	-0.0174	0.2204	-12.7876	6.8552	42.5089
4	2.75	-0.3995	-0.2859	2.0353	0.697	2.734	0.0941	0.1104	-0.1596	-0.1529	-0.2472	0.1618	-0.1556	-0.4336	0.0641	0.1222	0.0376	-0.0298	0.147	-0.0366	0.205	-15.5204	8.038	28.4282
5	1.4154	0.6131	0.2724	1.8351	0.8119	2.045	0.0321	-0.1542	-0.0338	0.0571	-0.047	-0.0404	-0.0225	0.0172	-0.0222	0.0713	0.0113	-0.0017	0.07	-0.023	0.0927	1.8514	9.358	39.9063
6	0.9908	0.1682	-0.4722	0.7689	0.0991	1.3945	-0.0513	-0.1372	-0.1318	-0.106	-0.0064	0.0074	0.1057	0.0498	0.0273	0.099	0.021	0.0127	0.0887	-0.0063	0.1435	2.5069	-0.006	28.1338
7	5.0999	-1.7923	0.0075	4.6521	0.2913	1.924	0.3753	0.1451	0.1632	-0.3922	0.012	0.2736	-0.3978	0.1604	-0.1821	0.1965	-0.0005	0.0456	0.1521	-0.0051	0.196	4.7061	15.5954	23.3762
8	0.9565	1.7193	0.0682	3.1883	0.3776	0.6366	-0.0414	0.4613	-0.1797	-0.1329	0.0831	0.1071	0.0183	-0.0586	-0.028	0.2053	-0.0204	0.0352	0.2228	-0.0507	0.2132	9.2194	5.0764	16.9727
9	1.4166	-0.8386	-0.7618	3.1455	1.1437	0.9814	0.0397	0.2844	0.0439	-0.3775	-0.1215	-0.06	-0.1199	-0.0866	0.0575	0.1348	0.0109	-0.0055	0.1509	0.0185	0.1695	-3.4126	4.5496	21.7738
10	1.1753	-0.1225	0.5967	0.4929	0.8442	3.9453	-0.0529	-0.0051	0.4997	-0.165	-0.0668	0.1599	-0.4746	0.1186	0.036	0.1615	0.0095	-0.0227	0.1049	-0.02	0.277	-4.0001	18.4347	34.1849
11	4.1364	3.1975	-2.2262	3.1304	-2.0132	1.3893	-0.0227	0.0887	-0.5006	0.0629	0.1122	-0.0403	0.2232	-0.238	-0.0932	0.2191	-0.0258	-0.0348	0.1784	0.0252	0.2366	27.4407	-5.8207	81.5507
12	1.391	0.436	0.4998	1.3271	0.1276	2.0763	-0.0318	-0.0807	-0.0517	0.1101	0.0467	-0.1282	0.1466	0.1718	-0.0156	0.1483	-0.006	-0.0098	0.1277	-0.0147	0.1519	35.6474	4.6061	82.369
13	1.2094	-0.096	0.4137	0.548	0.1744	2.7511	-0.0737	-0.1057	-0.0287	0.0899	-0.0675	0.0819	-0.0584	-0.3682	0.1198	0.1876	0.0179	0.0021	0.1848	-0.0417	0.2115	15.4524	6.9357	72.0594
14	1.6957	0.6617	0.689	1.6705	1.1372	2.6854	-0.0271	-0.1058	-0.0059	-0.0005	-0.0322	0.036	-0.1154	0.1292	0.0955	0.1458	0.0122	0.0092	0.1004	-0.0082	0.1047	31.1591	10.2386	75.0623
15	1.1081	0.6081	-0.0828	1.2913	0.2066	1.4668	0.0806	0.017	-0.068	-0.0331	-0.0398	-0.0645	-0.0744	0.0428	-0.0589	0.1589	0.0359	-0.0137	0.1301	-0.0246	0.113	30.5515	5.9703	65.7789
16	0.9624	0.8321	0.2804	2.2172	0.468	1.8113	0.161	0.1428	-0.0832	0.0277	-0.0867	0.0245	0.0791	0.3291	-0.0553	0.1303	0.0264	-0.0042	0.169	-0.0394	0.1447	33.8949	2.9434	61.2488
17	0.198	0.4506	0.0132	1.5684	-0.4026	0.3579	0.0383	0.2547	0.0014	-0.3688	0.0772	-0.0671	-0.0898	0.1264	-0.0805	0.1767	-0.0054	0.0106	0.2117	-0.0293	0.1557	32.6855	4.4791	54.7384
18	0.6467	-0.3729	-1.0901	1.3306	1.047	2.314	-0.1532	0.066	0.4734	-0.2011	-0.1525	-0.012	-0.7363	-0.1163	0.2131	0.243	0.0338	-0.0882	0.1259	0.0029	0.2699	24.4783	18.1401	68.2367
19	2.1124	-0.6367	0.0992	2.3365	0.3381	1.6786	0.0388	0.195	0.5495	-0.0196	0.1605	0.026	-0.4044	-0.2013	-0.0879	0.1981	0.0224	0.0026	0.1453	0.0598	0.2119	-18.9844	30.659	56.4881
20	1.7841	-0.0761	0.7495	1.9337	-0.6152	3.1027	0.1036	0.0625	0.1432	-0.0916	0.0542	0.2484	0.1121	-0.3747	-0.1413	0.0966	-0.0036	0.0336	0.1666	0.0141	0.1616	-23.7096	22.7241	58.4371
21	1.3972	0.3619	0.692	1.497	0.8622	0.8676	0.0635	-0.2695	0.2546	0.0849	-0.1508	0.2144	-0.0416	-0.2578	0.0289	0.2412	0.0076	0.0428	0.2403	-0.0109	0.2614	-20.801	21.9983	74.7129
22	4.3746	-0.0186	-0.3546	1.3678	0.2626	2.1754	-0.0144	-0.1858	0.0493	0.161	0.038	0.0142	0.119	0.0235	-0.0284	0.1769	-0.044	-0.006	0.1859	-0.0055	0.1051	-7.4747	21.141	79.9611
23	1.9029	0.6558	0.4309	1.1375	0.8413	1.8031	0.029	0.101	-0.0229	0.0003	-0.0269	0.0688	0.046	-0.1584	0.0095	0.0953	-0.0054	-0.0013	0.103	0.0208	0.1148	-15.8032	18.8505	60.8651
24	1.5846	0.0765	-0.0083	1.4049	0.1591	0.8733	0.0005	0.1199	0.2434	0.008	0.0081	0.0675	-0.0771	-0.0616	-0.0322	0.1069	-0.0199	-0.001	0.0881	0.0162	0.1411	-4.1534	28.1009	61.615
25	2.4382	0.9965	-1.1396	3.8432	-0.3834	3.9563	0.1301	0.0636	-0.1599	0.0379	-0.0113	-0.167	0.2266	0.1545	-0.128	0.1194	-0.0125	-0.0045	0.1268	-0.0213	0.1543	0.8208	12.7535	61.3836
26	0.4249	0.2918	0.3447	5.3882	2.3655	1.1428	0.1923	0.0573	-0.0248	-0.1892	0.0659	-0.6179	-0.1679	0.0813	-0.1465	0.1609	-0.017	0.0203	0.1602	-0.0255	0.2789	8.1295	23.0026	57.579
27	1.5488	1.7701	-1.1136	3.444	-1.4591	0.8139	-0.0496	-0.4687	-0.2299	-0.2018	-0.242	-0.4419	0.0867	0.2658	0.1667	0.1043	0.009	0.0218	0.1433	0.0323	0.141	1.4932	24.7099	69.0862
28	2.2022	0.672	0.7675	0.8733	0.5646	1.7913	0.3057	0.0382	-0.4486	0.1291	0.0765	0.0717	0.706	-0.0825	-0.2727	0.2839	-0.0265	-0.0564	0.1323	0.0192	0.1864	-10.9631	10.1228	68.0572
29	2.3927	-1.0231	-0.4699	3.7411	1.2183	2.4549	-0.2116	-0.276	0.6164	0.2443	0.0459	0.1976	-0.4596	-0.092	0.1666	0.2535	0.0391	-0.0395	0.206	-0.0247	0.2915	21.4919	31.9065	25.5195
30	1.6363	0.9488	-0.0653	1.1014	0.1999	1.8901	0.0563	-0.0186	0.2384	0.0635	-0.0932	0.1602	-0.0937	-0.2315	0.053	0.1276	0.0041	0.0067	0.1708	-0.0011	0.2059	19.5953	23.2797	29.2621
31	1.526	0.7338	0.1179	0.9297	0.443	1.632	0.1619	-0.2217	0.0533	0.1867	-0.1758	0.0038	0.1178	-0.1689	0.0042	0.1244	-0.0362	-0.0006	0.1225	0.0049	0.1038	28.4983	20.1854	35.196
32	0.978	0.1062	0.3521	1.1283	0.7345	0.5387	-0.0034	-0.0423	0.0644	-0.0765	-0.0972	0.1035	-0.064	-0.0288	0.0552	0.1022	-0.0273	0.002	0.0971	0.0184	0.1106	36.4596	29.0753	27.0908
33	2.3575	0.1381	-0.6969	4.9976	-1.5891	5.3271	0.2898	-0.2093	-0.3385	0.2323	-0.1494	-0.0446	-0.0934	0.526	-0.1252	0.1109	-0.0318	-0.0241	0.1309	0.0185	0.1715	42.3579	13.8459	26.4005
34	0.5072	-0.0369	0.149	1.719	0.5344	0.4526	0.0388	-0.031	-0.093	-0.0925	0.0952	-0.3575	-0.0345	0.0466	-0.1266	0.1096	-0.0092	0.0142	0.1206	-0.0017	0.1574	46.0395	24.8757	28.2571
35	2.593	0.5249	0.1396	0.4818	0.9386	2.1658	0.1322	0.0481	-0.5154	0.3504	-0.0687	-0.2096	0.4068	-0.1644	-0.1146	0.2005	-0.0138	-0.029	0.1292	0.0415	0.1809	30.779	10.0777	32.5562

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 52 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 53 through 77 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 78 through 102 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 103 through 119 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 120 through 143 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 144 through 189 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 190 through 203 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 204 through 224 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 225 through 238 )	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 239 through 254 )	A
11	X-RAY DIFFRACTION	11	chain 'B' and (resid -3 through 52 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 53 through 77 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 78 through 119 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 120 through 143 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 144 through 163 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 164 through 203 )	B
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 204 through 238 )	B
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 239 through 253 )	B
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 38 through 61 )	C
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 62 through 77 )	C
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 78 through 102 )	C
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 103 through 119 )	C
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 120 through 143 )	C
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 144 through 189 )	C
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 190 through 203 )	C
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 204 through 224 )	C
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 225 through 238 )	C
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 239 through 254 )	C
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 37 through 53 )	D
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 54 through 99 )	D
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 100 through 143 )	D
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 144 through 189 )	D
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 190 through 203 )	D
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 204 through 238 )	D
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 239 through 255 )	D

-
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