PDB-3mqq: The Crystal Structure of the PAS domain in complex with Ethanol o...

ID or keywords:

Entry

Database: PDB / ID: 3mqq

Title

The Crystal Structure of the PAS domain in complex with Ethanol of a Transcriptional Regulator in the LuxR family from Burkholderia thailandensis to 1.65A

Components

Transcriptional regulator, LuxR family

Keywords

Transcription regulator / PAS domain / LuxR / regulator / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative

Function / homology

Function and homology information

regulation of DNA-templated transcription / DNA binding
Similarity search - Function

Biological species

Burkholderia thailandensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.65 Å

Authors

Stein, A.J. / Tesar, C. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The Crystal Structure of the PAS domain in complex with Ethanol of a Transcriptional Regulator in the LuxR family from Burkholderia thailandensis to 1.65A
Authors: Stein, A.J. / Tesar, C. / Buck, K. / Joachimiak, A.

History

Deposition	Apr 28, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 23, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Jun 20, 2012	Group: Database references
Revision 1.3	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.4	Oct 30, 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 / struct_conn / struct_site 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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.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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3mqq.cif.gz	111.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3mqq.ent.gz	88.7 KB	Display	PDB format
PDBx/mmJSON format	3mqq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3mqq_validation.pdf.gz	453.7 KB	Display	wwPDB validaton report
Full document	3mqq_full_validation.pdf.gz	458.1 KB	Display
Data in XML	3mqq_validation.xml.gz	13.5 KB	Display
Data in CIF	3mqq_validation.cif.gz	16.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mq/3mqq ftp://data.pdbj.org/pub/pdb/validation_reports/mq/3mqq	HTTPS FTP

-
Related structure data

Related structure data	3mqo
Similar structure data	3mqo-d 4hbm-10 6j4b-1 5wse-1 2rf6-d 3jrz-1 4raj-d 5trf-8 6l2f-d 2hqz-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC67393.1

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#183 - Mar 2015 Phototropin similarity (1) #207 - Mar 2017 Photoactive Yellow Protein similarity (1) #13 - Jan 2001 Alcohol Dehydrogenase similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #44 - Aug 2003 Calmodulin similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#183 - Mar 2015
Phototropin
similarity (1)
#207 - Mar 2017
Photoactive Yellow Protein
similarity (1)
#13 - Jan 2001
Alcohol Dehydrogenase
similarity (1)
#191 - Nov 2015
Glutamate-gated Chloride Receptors
similarity (1)
#233 - May 2019
S-Nitrosylated Hemoglobin
similarity (1)
#44 - Aug 2003
Calmodulin
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Transcriptional regulator, LuxR family

B: Transcriptional regulator, LuxR family

hetero molecules

27.4 kDa, 2 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)	57.438, 35.726, 66.986
Angle α, β, γ (deg.)	90.000, 91.490, 90.000
Int Tables number	3
Space group name H-M	P121

#1: Protein	Transcriptional regulator, LuxR family Mass: 13481.028 Da / Num. of mol.: 2 / Fragment: sequence database residues 2-121 Source method: isolated from a genetically manipulated source Details: pMCSG7 / Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH_I2609 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2SVC5
#2: Chemical	ChemComp-EOH / ETHANOL Mass: 46.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 68 / 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	Density Matthews: 2.6 Å³/Da / Density % sol: 56.7 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 30% ethanol, 20% PEG 4000, 0.1M Sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9794 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 27, 2010

Radiation

Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9794 Å / Relative weight: 1

Reflection

Resolution: 1.65→50 Å / Num. obs: 32890 / % possible obs: 99.2 % / Redundancy: 3.7 % / R_merge(I) obs: 0.085 / Χ²: 2.372 / Net I/σ(I): 8.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.65-1.71	3.7	0.627	3244	0.931	1	99
1.71-1.78	3.7	0.455	3250	0.959	1	99
1.78-1.86	3.7	0.297	3270	1.025	1	99.3
1.86-1.96	3.7	0.211	3248	1.207	1	99.5
1.96-2.08	3.7	0.147	3292	1.441	1	99.5
2.08-2.24	3.7	0.113	3320	1.832	1	99.7
2.24-2.46	3.7	0.097	3270	2.334	1	99.9
2.46-2.82	3.7	0.092	3332	3.381	1	100
2.82-3.55	3.6	0.074	3341	4.248	1	99.7
3.55-50	3.5	0.072	3323	6.664	1	96.5

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.004	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Resolution: 1.65→33.48 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.928 / SU B: 4.915 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.257	1667	5.1 %	RANDOM
R_work	0.224	-	-	-
obs	0.225	32814	98.81 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 29.769 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.21 Å²	0 Å²	0.16 Å²
2-	-	0.3 Å²	0 Å²
3-	-	-	-0.08 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→33.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1801	0	26	68	1895

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	1887
X-RAY DIFFRACTION	r_angle_refined_deg	1.318	1.954	2553
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.942	5	241
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	25.869	21.591	88
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.262	15	301
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.779	15	23
X-RAY DIFFRACTION	r_chiral_restr	0.101	0.2	284
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	1443
X-RAY DIFFRACTION	r_mcbond_it	0.6	1.5	1167
X-RAY DIFFRACTION	r_mcangle_it	0.94	2	1869
X-RAY DIFFRACTION	r_scbond_it	1.984	3	720
X-RAY DIFFRACTION	r_scangle_it	2.74	4.5	678

LS refinement shell

Resolution: 1.649→1.692 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.325	114	-
R_work	0.296	2238	-
all	-	2352	-
obs	-	-	96.39 %

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	10.3245	-10.1321	3.1804	24.9707	0.5268	8.3523	0.3974	0.0031	-0.5681	-0.4146	-0.4154	1.5377	0.144	-0.547	0.0181	0.0949	-0.0672	0.0047	0.3316	-0.0067	0.2296	5.5456	-19.3067	18.3361
2	19.1267	1.0052	-0.8174	11.3199	1.9375	0.2101	-0.2657	-0.2984	-0.275	-0.1577	0.2096	0.2338	0.0578	-0.0309	0.0561	0.1503	-0.1602	-0.0377	0.2997	-0.0017	0.0661	13.9492	-21.3663	18.0098
3	1.2574	-3.5464	0.8705	11.6538	2.5617	9.8683	0.0069	-0.0048	-0.0018	-0.0528	-0.0967	0.0875	0.0576	-0.2022	0.0898	0.0224	-0.0237	-0.0042	0.1368	-0.017	0.0536	19.643	-15.4498	20.8678
4	4.1478	-0.471	-0.1119	15.2706	0.5365	8.7145	0.0425	-0.5468	0.3976	0.4124	-0.2287	0.2982	-0.3533	-0.1877	0.1862	0.0803	0.0009	-0.0068	0.1727	-0.0401	0.0574	24.4956	-9.934	29.7634
5	6.8596	-0.8471	-2.769	12.6663	5.0222	12.9782	0.0771	-0.2689	-0.2757	0.4005	-0.1977	-0.1225	0.4559	-0.4474	0.1207	0.0493	-0.0235	-0.0017	0.1267	0.007	0.0605	19.1317	-20.4509	23.73
6	12.2766	-3.7323	1.6724	1.4954	-1.3394	1.8745	-0.3546	-0.2864	-0.591	-0.0645	0.0596	-0.0786	0.3036	-0.0188	0.2949	0.182	0.0148	0.0543	0.0417	0.0286	0.2596	27.05	-24.4809	20.0024
7	2.1663	-8.6291	-3.5678	30.1568	3.1727	15.4517	-0.2038	0.0616	-0.044	0.6107	-0.3037	-0.376	0.3561	-0.273	0.5075	0.2162	-0.0404	-0.0444	0.2717	0.0503	0.1521	23.6153	-24.7145	27.9396
8	13.5978	8.8426	-5.8367	6.3271	-6.0715	10.6865	0.1767	0.0972	-0.5114	0.0506	0.0605	-0.2034	0.3284	-0.0791	-0.2371	0.1272	-0.0187	-0.0039	0.1523	-0.0109	0.0815	25.8922	-17.1722	29.8261
9	7.9897	-3.3931	-7.7451	10.0375	6.1938	12.4258	-0.2383	-0.2971	-0.0052	0.2436	0.0299	-0.2293	0.3986	0.473	0.2084	0.0767	0.0035	-0.0157	0.1737	0.016	0.0959	34.2323	-15.9475	24.8612
10	6.1888	-0.5505	0.1677	15.6072	-0.1739	-0.515	-0.3319	0.0147	0.5881	0.0234	0.2935	-0.536	0.004	0.0758	0.0384	0.0372	0.023	-0.0002	0.4213	0.0036	0.1846	38.6112	-9.9591	24.4397
11	16.983	1.6435	2.9077	39.0965	0.7083	-1.3536	0.4461	0.1905	0.8875	-0.8603	-0.6032	0.1223	0.0627	0.1097	0.1572	0.1518	-0.0438	-0.019	0.3136	0.0278	0.2828	33.8129	-3.8764	20.0746
12	2.0957	4.1224	-4.4925	18.2337	-3.9673	11.2561	-0.0304	0.0166	-0.1199	0.1078	-0.0134	-0.3203	0.17	-0.0269	0.0438	0.1243	0.026	-0.0233	0.1296	-0.0012	0.2927	27.2147	1.7024	18.6357
13	15.3292	-17.9068	-5.5497	20.7117	6.5794	3.7954	0.0865	0.2817	0.5125	-0.1372	-0.2919	-0.554	-0.486	0.0209	0.2053	0.1506	-0.0266	-0.0158	0.106	0.0248	0.2393	26.1508	-3.593	14.1562
14	2.3085	1.889	-0.8085	4.8264	-3.3617	3.3416	0.0064	-0.2864	-0.0452	0.6425	0.0215	-0.0632	-0.2165	0.0466	-0.0279	0.2121	0.076	-0.0098	0.1831	0.0138	0.1378	34.1402	-17.5492	17.2234
15	11.5762	-2.123	-1.7343	9.1097	-5.9441	15.5809	-0.0581	-0.1714	-0.7942	-0.3224	-0.4094	-0.5433	1.1234	0.5208	0.4676	0.1436	0.0498	0.0065	0.1132	-0.0082	0.2344	36.1033	-23.9936	18.8463
16	7.9278	-4.1285	-1.9062	4.2496	1.4276	3.4305	0.0369	0.1255	0.1519	-0.0586	-0.13	0.0938	-0.1216	0.041	0.0931	0.0208	-0.0161	0.0223	0.0982	0.0134	0.0851	24.7997	-9.0936	16.4596
17	0.3059	0.2795	-1.0074	14.256	-5.0887	10.1055	-0.0679	-0.1325	0.2001	0.0404	-0.0059	-0.2448	-0.405	-0.0822	0.0738	0.1225	0.0274	-0.0821	0.1716	-0.0901	0.2591	23.0954	0.5267	23.8508
18	5.5244	-4.845	-3.9905	3.9657	2.6173	9.3704	-0.0995	0.0368	0.196	0.0528	-0.0498	-0.1651	0.1695	-0.0339	0.1492	0.0146	-0.0137	0.0114	0.1058	-0.0651	0.1196	20.9146	-9.7804	20.7649
19	10.6855	-0.6386	-2.8031	16.7481	-3.7876	7.7109	0.0673	0.7394	-0.5216	-0.8774	-0.1302	-0.3305	0.4926	0.4512	0.0629	0.0702	0.0291	0.022	0.1821	-0.0212	0.1006	28.1431	-19.9573	11.9814
20	4.1456	1.8002	-0.1018	9.4345	-3.861	14.6923	0.0216	-0.4976	0.3289	0.6293	0.1631	0.4326	-0.2666	-0.3866	-0.1847	0.101	0.0131	0.0417	0.2462	-0.0121	0.1015	9.962	-11.3144	22.034
21	3.6536	0.916	-0.4329	8.7001	5.5208	10.4671	0.0978	-0.2654	0.3555	0.2882	0.0631	-0.0832	0.0171	-0.0251	-0.1608	0.0377	-0.011	0.0138	0.1066	0.0022	0.0689	13.4792	-10.0383	13.5606
22	3.5093	-0.9575	2.0692	7.5206	4.6525	18.4598	0.1912	-0.1185	-0.4618	-0.161	-0.1489	0.4585	0.6057	-0.7507	-0.0423	0.1122	-0.0444	-0.0381	0.1544	0.0175	0.1202	4.0155	-21.1505	5.704
23	8.7763	3.0828	6.3433	8.6375	5.8932	9.8117	0.184	-0.3537	0.0163	0.3786	-0.2026	0.3395	0.0666	-0.7381	0.0186	0.0354	-0.0018	0.0107	0.1723	0.0055	0.0882	3.2222	-15.2093	8.0732
24	6.5047	2.5691	-7.711	8.0711	-3.9121	21.4228	0.2949	-0.1626	0.699	-0.2645	-0.2842	-0.3038	-0.455	-0.1842	-0.0108	0.0881	0.006	0.0257	0.0611	-0.0175	0.1736	11.6291	-6.3038	8.668
25	3.7541	-2.419	-4.7883	3.1662	3.2484	7.7848	0.0606	0.3219	0.345	-0.0851	-0.0484	0.026	-0.2974	-0.2896	-0.0122	0.2214	0.0209	0.0047	0.0836	0.0565	0.2167	11.4782	-4.719	2.18
26	18.7046	8.1542	3.6918	34.8892	2.3584	5.5256	0.2436	-0.4983	0.5859	0.1477	-0.3512	0.3447	-0.402	-0.3582	0.1076	0.0802	0.0349	-0.0331	0.1478	-0.0281	0.1373	3.0425	-7.3387	5.9744
27	9.9298	-3.8562	-4.1114	7.3059	-0.5506	9.9506	-0.1981	0.2452	0.1351	-0.1059	-0.1441	-0.0707	0.2225	0.0348	0.3422	0.0697	-0.0004	-0.0458	0.1418	-0.0058	0.0901	4.3516	-14.8666	-0.6707
28	14.4675	4.6011	0.616	8.2572	-0.0944	10.4918	0.1056	-0.1852	0.2487	-0.2177	0.0439	0.4902	-0.0834	0.0362	-0.1494	0.0544	0.0055	0.0181	0.1323	0.008	0.1324	10.5411	-14.2203	-5.4051
29	7.7014	-3.4891	-4.8793	8.4552	0.7186	7.3051	-0.2032	0.3265	0.1251	-0.376	0.2903	-0.246	0.6302	0.1263	-0.0871	0.169	-0.0183	-0.0075	0.2264	0.0064	0.1285	11.0455	-20.632	-8.814
30	-0.3352	1.2546	5.6704	43.9118	-6.1088	32.7567	0.4486	0.2542	0.0295	0.1811	-0.5868	0.4018	1.7248	0.5711	0.1382	0.5885	0.3116	-0.0325	0.4552	-0.0944	0.1262	13.5633	-26.7117	-2.868
31	10.12	0.1301	5.4166	8.535	-1.3869	11.4176	0.3104	-0.0794	0.029	-0.4393	-0.0621	-0.522	0.2681	0.5753	-0.2483	0.3362	0.0422	-0.0067	0.1758	0.0191	0.2204	16.6932	-32.1012	4.3738
32	11.5159	13.968	-7.2265	38.7369	-25.7264	17.631	0.4279	0.2911	-0.2081	-0.7425	-0.1301	0.3423	0.7979	0.3463	-0.2978	0.2664	0.1288	0.0604	0.2466	-0.02	0.0814	19.5947	-23.298	3.7915
33	13.2922	-9.3331	1.3324	9.9132	2.6689	5.2327	0.3524	0.1162	-0.6658	-0.1775	-0.4013	0.9944	0.0658	-0.2067	0.0489	0.1641	0.0092	0.023	0.1818	-0.0349	0.2544	15.8771	-11.539	-3.6753
34	6.3778	-0.3685	1.1376	1.1863	0.4114	7.1132	-0.023	0.1967	0.293	-0.2028	0.0157	0.1211	-0.6074	0.158	0.0074	0.1515	-0.0319	0.0251	0.1137	0.0115	0.0797	18.1419	-9.4165	-3.1601
35	8.0306	2.6283	-3.1327	4.8762	-3.345	4.7999	0.2336	-0.1679	-0.2921	0.1405	-0.1022	0.0402	0.4206	-0.0292	-0.1315	0.1653	-0.0308	-0.0145	0.0853	-0.0074	0.0771	12.9213	-25.0685	9.8161
36	0.532	0.6534	-0.2661	1.4977	1.8065	3.8369	0.0375	0.0446	-0.2063	-0.1158	-0.0462	-0.1804	0.0282	-0.1091	0.0087	0.406	-0.024	-0.1276	0.1084	-0.0013	0.1925	8.5859	-29.6199	6.8879
37	8.0932	6.735	-3.9745	8.519	-4.292	6.0038	-0.1269	0.1729	0.1669	-0.1852	0.1073	-0.0765	-0.0007	0.0978	0.0197	0.0578	-0.011	0.0375	0.0984	-0.0126	0.0628	17.6717	-13.6788	5.8456
38	1.5131	-2.6879	5.2601	20.4674	-7.8223	17.3859	-0.3113	0.1121	0.2129	0.7983	-0.2625	-0.3605	-0.9143	0.3625	0.5738	0.1169	-0.0234	0.062	0.2443	0.0002	0.2584	32.1914	-7.106	8.5861

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 8
2	X-RAY DIFFRACTION	2	A	9 - 14
3	X-RAY DIFFRACTION	3	A	15 - 20
4	X-RAY DIFFRACTION	4	A	21 - 25
5	X-RAY DIFFRACTION	5	A	26 - 31
6	X-RAY DIFFRACTION	6	A	32 - 37
7	X-RAY DIFFRACTION	7	A	38 - 43
8	X-RAY DIFFRACTION	8	A	44 - 48
9	X-RAY DIFFRACTION	9	A	49 - 53
10	X-RAY DIFFRACTION	10	A	54 - 60
11	X-RAY DIFFRACTION	11	A	61 - 65
12	X-RAY DIFFRACTION	12	A	66 - 71
13	X-RAY DIFFRACTION	13	A	72 - 77
14	X-RAY DIFFRACTION	14	A	78 - 83
15	X-RAY DIFFRACTION	15	A	84 - 89
16	X-RAY DIFFRACTION	16	A	90 - 99
17	X-RAY DIFFRACTION	17	A	100 - 105
18	X-RAY DIFFRACTION	18	A	106 - 110
19	X-RAY DIFFRACTION	19	A	111 - 116
20	X-RAY DIFFRACTION	20	B	4 - 10
21	X-RAY DIFFRACTION	21	B	11 - 18
22	X-RAY DIFFRACTION	22	B	19 - 23
23	X-RAY DIFFRACTION	23	B	24 - 28
24	X-RAY DIFFRACTION	24	B	29 - 34
25	X-RAY DIFFRACTION	25	B	35 - 39
26	X-RAY DIFFRACTION	26	B	40 - 44
27	X-RAY DIFFRACTION	27	B	45 - 49
28	X-RAY DIFFRACTION	28	B	50 - 54
29	X-RAY DIFFRACTION	29	B	55 - 60
30	X-RAY DIFFRACTION	30	B	61 - 66
31	X-RAY DIFFRACTION	31	B	67 - 72
32	X-RAY DIFFRACTION	32	B	73 - 78
33	X-RAY DIFFRACTION	33	B	79 - 83
34	X-RAY DIFFRACTION	34	B	84 - 92
35	X-RAY DIFFRACTION	35	B	93 - 99
36	X-RAY DIFFRACTION	36	B	100 - 107
37	X-RAY DIFFRACTION	37	B	108 - 116
38	X-RAY DIFFRACTION	38	B	117 - 121

-
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