PDB-2hrt: Asymmetric structure of trimeric AcrB from Escherichia coli

ID or keywords:

Entry

Database: PDB / ID: 2hrt

Title

Asymmetric structure of trimeric AcrB from Escherichia coli

Components

Acriflavine resistance protein B

Keywords

MEMBRANE PROTEIN / TRANSPORT PROTEIN / AcrB / multidrug efflux pump / RND / antibiotic resistance / AcrA / TolC / proton-coupled exchanger

Function / homology

Function and homology information

alkane transmembrane transporter activity / alkane transport / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / bile acid transmembrane transporter activity / xenobiotic transport / bile acid and bile salt transport ...
Similarity search - Function

Biological species

Escherichia coli K12 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Seeger, M.A. / Schiefner, A. / Eicher, T. / Verrey, F. / Diederichs, K. / Pos, K.M.

Citation

Journal: Science / Year: 2006
Title: Structural Asymmetry of AcrB Trimer Suggests a Peristaltic Pump Mechanism.
Authors: Seeger, M.A. / Schiefner, A. / Eicher, T. / Verrey, F. / Diederichs, K. / Pos, K.M.

History

Deposition	Jul 20, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 12, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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	2hrt.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb2hrt.ent.gz	916.5 KB	Display	PDB format
PDBx/mmJSON format	2hrt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hr/2hrt ftp://data.pdbj.org/pub/pdb/validation_reports/hr/2hrt	HTTPS FTP

-
Related structure data

Related structure data	2gifC 1iwgS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2drd-d 1t9y-1 3aoa-d 6iia-1 2dr6-d 2hqf-1 3w9j-1 7kgi-d 3w9j-2 1t9w-1 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#95 - Nov 2007 Multidrug Resistance Transporters similarity (5) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#95 - Nov 2007
Multidrug Resistance Transporters
similarity (5)
#129 - Sep 2010
Isocitrate Dehydrogenase
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#191 - Nov 2015
Glutamate-gated Chloride Receptors
similarity (1)
#215 - Nov 2017
Aspartate Transcarbamoylase
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)

Deposited unit

A: Acriflavine resistance protein B

B: Acriflavine resistance protein B

C: Acriflavine resistance protein B

D: Acriflavine resistance protein B

E: Acriflavine resistance protein B

F: Acriflavine resistance protein B

hetero molecules

689 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Acriflavine resistance protein B

B: Acriflavine resistance protein B

C: Acriflavine resistance protein B

hetero molecules

defined by author&software
345 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Acriflavine resistance protein B

E: Acriflavine resistance protein B

F: Acriflavine resistance protein B

hetero molecules

defined by author&software
345 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	127.330, 134.870, 140.840
Angle α, β, γ (deg.)	103.90, 94.64, 90.11
Int Tables number	1
Space group name H-M	P1

Details

The biological unit is a trimer. There are 2 biological units (trimers) in the asymmetric unit (chains A, B, C and chains D, E, F)

#1: Protein	Acriflavine resistance protein B Mass: 114736.289 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: acrB, acrE / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P31224
#2: Chemical	ChemComp-FLC / CITRATE ANION Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₅O₇

#1: Protein

Acriflavine resistance protein B

Mass: 114736.289 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: acrB, acrE / Plasmid: pET24 / Production host:

Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P31224

#2: Chemical

ChemComp-FLC / CITRATE ANION

Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₅O₇

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.49 Å³/Da / Density % sol: 64.78 %
Crystal grow	Temperature: 290 K / pH: 4.6 Details: 5 % polyethylene glycol 400, 16-22 % polyethylene glycol 300, 8-11 % glycerol, 70 mM Nacitrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 4.60

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9737
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 9, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9737 Å / Relative weight: 1
Reflection	Resolution: 3→29.8 Å / Num. obs: 181133 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / R_merge(I) obs: 0.134 / Net I/σ(I): 8.4
Reflection shell	Resolution: 3→3.1 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.763 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

-
Phasing

Phasing MR

R_factor: 0.368 / Cor.coef. F_o:F_c: 0.671

	Highest resolution	Lowest resolution
Rotation	5 Å	29.8 Å
Translation	5 Å	29.8 Å

-
Processing

Software

Name	Version	Classification
MOLREP		phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IWG

1iwg

Resolution: 3→29.8 Å / Cor.coef. F_o:F_c: 0.91 / Cor.coef. F_o:F_c free: 0.879 / SU B: 48.918 / SU ML: 0.396 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.274	9081	5 %	RANDOM
R_work	0.231	-	-	-
obs	0.234	181137	99.9 %	-
all	-	172056	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 51.41 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.01 Å²	-0.01 Å²	-0.19 Å²
2-	-	-0.08 Å²	0.08 Å²
3-	-	-	0.07 Å²

Refinement step

Cycle: LAST / Resolution: 3→29.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	47046	0	52	0	47098

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	47994
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.059	1.968	65180
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.092	5	6186
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.535	24.537	1878
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.001	15	8064
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.818	15	222
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	7672
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	35610
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.197	0.2	23793
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.3	0.2	33666
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.121	0.2	1300
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.196	0.2	77
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.08	0.2	7
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.197	1.5	31455
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.354	2	49508
X-RAY DIFFRACTION	r_scbond_it	0.432	3	18540
X-RAY DIFFRACTION	r_scangle_it	0.744	4.5	15672
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 3→3.08 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.376	683	-
R_work	0.332	12568	-
obs	-	-	99.81 %

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	2.2138	0.0786	-1.0945	1.6621	0.3995	2.305	0.0027	-0.6092	0.0875	0.2129	0.0864	0.183	-0.1671	-0.204	-0.0891	0.0841	0.0725	-0.0286	0.2445	-0.0763	-0.2801	1.209	8.2197	36.736
2	3.629	1.0434	-2.9252	5.5545	-0.5691	6.4203	0.1627	0.1468	0.1896	-0.0594	-0.0208	-0.1918	-0.217	-0.1831	-0.1419	-0.5716	0.0265	-0.0673	-0.6054	0.0344	-0.4618	14.8255	10.9212	-12.1504
3	3.3522	-1.0319	-1.5335	3.6679	0.396	4.1178	0.1138	-0.6531	-0.0637	0.2533	0.0064	-0.6917	-0.4256	0.5507	-0.1202	-0.3443	-0.0062	-0.0902	-0.3227	-0.0235	-0.2783	32.1833	0.7369	4.566
4	1.7005	0.6582	0.3032	2.6757	1.4899	1.3115	0.0677	0.1912	-0.4256	-0.6445	0.0211	-1.0984	-0.1663	0.2761	-0.0888	-0.2797	0.1068	0.1515	-0.4026	-0.0337	-0.0081	40.4093	-10.2217	-25.4578
5	3.002	0.4699	-2.8115	4.7335	0.1256	12.8187	0.3253	-0.8753	0.8313	0.2167	-0.1612	-0.0982	-1.3202	0.0938	-0.1641	0.1771	-0.2419	0.0217	-0.0273	-0.1731	0.0636	35.4486	20.5537	9.8276
6	4.569	0.1522	0.0746	5.0036	4.1616	4.2064	0.2767	-0.634	1.0071	0.2794	-0.0748	0.0669	-0.742	-0.0815	-0.2019	-0.2102	-0.0588	0.2039	-0.4727	-0.0794	0.1696	16.6373	34.0429	-5.1759
7	2.5506	0.4045	-0.74	4.2024	-1.7711	2.8329	0.0248	0.5063	0.1084	-0.6403	-0.0604	-0.4766	0.0874	0.2427	0.0356	-0.3289	-0.0127	0.2113	-0.3624	-0.0075	-0.0896	39.0097	11.3098	-27.6891
8	2.2166	-0.0028	-0.3227	0.8635	0.4965	2.3005	0.0209	-0.6467	0.6726	0.3963	-0.1111	-0.1802	-0.7194	-0.121	0.0902	0.4871	0.0916	0.0303	0.2529	-0.371	0.0967	-0.8685	27.8786	39.2573
9	1.6375	-0.1039	-1.6339	1.0078	0.0119	2.961	-0.0686	-0.2015	-0.398	0.2606	-0.0493	0.2589	0.4204	-0.6256	0.1179	0.0362	-0.1776	0.0217	0.2991	0.3046	-0.1404	-19.4834	-23.4062	22.0462
10	6.6711	-1.2596	-5.1276	3.0376	1.8374	5.4686	0.0599	0.256	-0.4395	-0.1793	-0.2822	0.1077	0.1341	-0.3455	0.2223	-0.4549	0.0356	-0.0695	-0.578	0.0508	-0.379	16.4465	-12.106	-10.0524
11	4.2643	-2.1121	-4.281	1.1057	1.877	5.2913	-0.3234	0.3069	-0.7649	-0.0521	-0.1655	0.2078	0.2127	-0.3735	0.4888	-0.1324	-0.115	-0.0457	-0.1557	0.0477	0.0848	-4.5606	-28.4917	-19.1394
12	1.3449	-0.9705	1.4425	5.2228	-1.5538	2.173	0.3482	1.0838	-0.4821	-1.0914	-0.4464	-0.0519	0.2925	0.06	0.0982	0.0137	0.0732	0.0221	0.0967	-0.0407	-0.3797	11.5135	-13.8566	-44.6741
13	5.0846	-0.0727	-2.9845	2.9845	-1.8287	6.0462	-0.1406	-0.5943	-0.8811	0.7174	0.0916	-0.2894	0.2032	0.0626	0.049	0.1064	-0.045	0.1055	-0.2602	0.0776	0.2803	7.5485	-43.4597	-8.5247
14	3.9461	0.1811	-0.2004	6.0304	-2.4592	6.3302	-0.1357	-0.9017	-0.5508	0.5816	-0.0437	-0.237	0.7277	0.0097	0.1795	-0.1839	0.1826	-0.0495	-0.3873	0.2164	-0.0547	27.4214	-27.6208	5.1131
15	4.2303	-2.2116	0.1134	1.6079	-0.2802	1.6329	0.0929	0.7956	0.0017	-0.7653	-0.2255	-0.4959	0.0586	0.0328	0.1325	-0.1871	-0.0127	0.1439	-0.3342	-0.1084	-0.1006	28.1015	-22.8372	-33.6634
16	0.9019	-0.1124	-0.395	1.5419	0.7494	2.7433	-0.1363	-0.4332	-0.5528	0.4933	0.0763	-0.1354	0.7815	-0.0974	0.06	0.5211	-0.0097	0.0108	0.2546	0.4169	0.0017	-7.0846	-32.0007	34.7545
17	3.2917	0.2985	-0.0782	1.9428	0.2036	2.1653	0.1348	-0.8333	0.3628	0.442	-0.0468	0.4772	-0.236	-0.6137	-0.088	-0.2263	0.2009	0.0387	0.2567	0.0319	-0.0832	-31.4775	16.6313	14.86
18	1.9968	-1.2071	-0.9096	1.4904	1.2788	14.1311	0.1155	0.3945	-0.1003	-0.3338	0.0337	-0.2776	0.3776	0.0775	-0.1492	-0.4198	-0.0494	-0.1159	-0.3441	0.0464	-0.2855	-2.3376	-3.8452	-20.1893
19	5.7923	1.5627	-2.1407	2.8544	-0.8895	2.2339	0.1728	0.4215	0.8661	-0.2664	0.0377	0.1556	-0.4566	-0.3169	-0.2105	-0.2457	0.2466	-0.0404	-0.3291	0.2443	-0.1635	-4.3122	24.1242	-21.6378
20	3.0707	0.9258	1.4785	1.5325	0.2615	3.3132	0.068	1.0148	0.5181	-0.7034	0.1361	-0.3093	-0.2746	0.3441	-0.2041	-0.0532	0.0144	0.2518	-0.2432	0.1402	-0.157	23.4687	18.2826	-38.2995
21	5.3825	-1.9541	-2.796	4.2818	2.8825	8.391	0.0612	0.4436	0.3114	-0.6978	0.0831	0.7173	-0.2633	-0.7375	-0.1444	-0.2065	0.2061	-0.2238	0.0834	0.3891	-0.0133	-22.7202	18.9082	-30.1102
22	6.2598	0.272	-1.3584	3.2003	-1.1212	4.4588	0.0958	0.5417	-0.4313	-0.3463	-0.2548	0.5012	0.1236	-0.9114	0.159	-0.3419	-0.0224	-0.3159	0.1756	0.0705	-0.3069	-24.7734	-3.8191	-28.1655
23	1.1631	-0.1259	-0.1975	0.6297	0.0477	3.3277	0.1143	0.9902	-0.0262	-0.6283	0.1467	-0.1412	-0.1362	-0.1453	-0.2611	0.085	0.1055	0.0577	0.1523	0.1329	-0.3984	8.6768	5.5297	-47.7666
24	3.7081	-0.2891	-1.2976	1.4761	0.2299	2.8422	0.1331	-0.4061	-0.0982	0.3846	-0.2148	0.7729	0.0036	-0.9103	0.0816	-0.2743	0.0329	0.01	0.5267	0.116	0.0724	-46.317	4.7202	8.3393
25	2.2356	-0.1923	-1.0554	1.4816	0.1179	2.1482	-0.0451	0.6488	0.2779	-0.4907	0.0838	-0.1673	-0.3557	0.2677	-0.0388	0.2496	-0.0803	-0.0296	0.3807	0.1966	-0.0805	-52.7457	75.5754	-77.9152
26	3.1127	-1.4396	-3.2548	4.7924	1.2782	6.4702	0.1838	-0.1151	0.2722	0.0282	0.0551	0.2454	-0.2814	0.1816	-0.2389	-0.5571	-0.048	-0.0564	-0.5538	-0.0201	-0.4007	-66.1897	78.4608	-28.9902
27	4.6722	2.0167	-0.8064	4.3817	-0.3108	3.1531	0.0441	0.6179	0.1379	-0.3734	0.0453	0.5535	-0.3477	-0.6228	-0.0894	-0.2996	0.0465	-0.098	-0.2684	0.1015	-0.3389	-83.4949	67.9552	-45.5651
28	1.191	-1.2551	0.4297	3.8981	-1.8066	2.242	0.1431	-0.094	-0.3145	0.576	-0.1534	0.7424	-0.0633	-0.4225	0.0103	-0.2365	-0.1956	0.157	-0.3973	0.0269	-0.038	-91.4654	57.1125	-15.4351
29	3.9671	-0.1172	-3.2687	2.7602	0.16	14.1943	0.4321	0.7496	0.9106	-0.2481	-0.1494	0.2428	-1.5783	-0.1424	-0.2827	0.2675	0.2545	-0.0533	-0.0976	0.1598	0.2629	-87.0171	87.6948	-50.944
30	3.9716	0.3061	0.2841	6.3112	-3.8148	4.4182	0.3392	0.7857	0.9409	-0.3102	-0.1448	-0.0346	-0.8827	0.115	-0.1944	-0.154	0.0523	0.2629	-0.4067	0.1184	0.2596	-68.3047	101.5099	-36.1098
31	2.1605	-0.755	-0.5494	5.1619	2.7643	2.6536	0.1201	-0.4487	0.1959	0.395	-0.203	0.359	0.1463	-0.4784	0.0829	-0.3738	-0.0271	0.2178	-0.321	-0.0109	-0.0418	-90.312	78.6742	-13.3521
32	1.3659	0.2494	-0.6174	0.9351	-0.228	1.3666	0.0957	0.6471	0.6941	-0.5281	-0.0432	0.2239	-0.6377	-0.0242	-0.0525	0.6135	-0.0478	0.0073	0.4331	0.4881	0.4125	-50.912	95.2391	-80.575
33	2.0986	0.1624	-2.2803	1.5492	0.2051	2.8817	-0.0601	0.215	-0.3695	-0.2237	0.0076	-0.2402	0.2259	0.2971	0.0525	-0.0656	0.0883	0.0137	0.1266	-0.1862	-0.2547	-31.6187	44.2995	-63.1044
34	5.4883	1.6435	-4.1242	2.9875	-1.1719	5.4861	0.0482	-0.2475	-0.4197	0.1853	-0.2667	-0.09	0.2547	0.4241	0.2185	-0.427	0.0015	-0.0559	-0.5488	-0.0034	-0.3919	-67.5462	55.4019	-30.9292
35	4.2578	1.9953	-4.3195	2.0101	-0.8427	7.4056	-0.3706	-0.5094	-0.736	0.1406	-0.0357	-0.2273	0.6497	0.8253	0.4064	0.1288	0.2715	-0.0108	-0.1175	0.1061	-0.1355	-46.3085	39.3292	-21.8233
36	2.0502	1.2961	0.449	4.7415	1.1294	1.5138	0.3478	-1.2481	-0.3854	0.9632	-0.4047	-0.1424	0.2428	0.1867	0.0569	0.1027	0.0153	-0.0837	0.1626	0.0717	-0.4207	-62.4486	53.9536	3.6822
37	4.325	0.2311	-3.2642	3.7292	1.4357	6.966	-0.2451	0.4412	-0.8105	-0.3743	0.1184	0.3555	0.5623	0.2192	0.1268	0.4206	0.1411	0.1347	-0.2244	0.0488	0.0932	-58.2833	24.1452	-32.2874
38	2.799	0.3728	-0.9442	5.4931	3.3112	6.7053	-0.1269	0.6807	-0.4302	-0.4499	-0.0068	0.2522	0.7632	0.0296	0.1337	-0.0791	-0.1841	-0.0027	-0.411	-0.1231	-0.1599	-78.3992	39.6526	-45.9451
39	3.1968	1.5352	0.6161	0.7601	0.0956	1.8726	0.0973	-0.6336	0.0295	0.6117	-0.1426	0.3521	0.186	0.0177	0.0453	-0.0826	0.0002	0.1473	-0.3255	0.1042	-0.135	-78.9747	44.7009	-7.1989
40	2.3258	-0.3509	-0.7667	2.1549	-0.3603	2.6042	-0.1267	0.7716	-0.4795	-0.4353	0.032	0.1053	0.5585	-0.2373	0.0947	0.3301	-0.0961	0.0867	0.2804	-0.3605	-0.1305	-43.9674	35.4704	-75.7029
41	2.6296	-0.1061	-0.9333	1.5458	-0.391	2.1293	0.1436	0.4392	0.5137	-0.4239	0.126	-0.349	-0.2638	0.2741	-0.2696	-0.1405	-0.2692	0.0867	0.1438	-0.1599	0.0447	-20.0706	84.5252	-56.234
42	2.8158	0.4812	-1.0918	2.0287	-1.2881	11.4079	0.0492	-0.4985	-0.1678	0.3226	0.1135	0.3085	0.4731	0.1991	-0.1627	-0.3749	0.0804	-0.1394	-0.2197	-0.0241	-0.2524	-48.8193	63.9546	-20.9269
43	6.0413	-1.6341	-1.8838	2.212	0.6943	3.4116	0.2425	-0.4739	0.8447	0.3368	0.0327	0.0364	-0.526	0.5211	-0.2752	-0.2503	-0.2899	0.0535	-0.2427	-0.3305	-0.0196	-47.1706	91.9548	-19.6718
44	3.5206	-0.5225	0.7191	1.5444	0.0275	2.723	-0.0171	-0.9814	0.4222	0.6181	0.2136	0.2102	-0.4464	-0.1174	-0.1965	-0.103	0.0078	0.2233	-0.1941	-0.2138	-0.1375	-74.8107	85.9041	-2.854
45	4.1531	1.5677	-2.2602	4.7284	-2.2246	8.7208	0.2901	-0.5047	0.1606	0.627	-0.06	-0.7066	-0.3024	1.0997	-0.23	-0.1768	-0.215	-0.1417	0.2846	-0.4547	-0.0076	-28.667	87.0158	-11.2432
46	5.2246	-0.4174	-0.8259	2.2665	1.1785	2.6815	-0.0648	-0.6632	-0.1363	0.4634	0.0296	-0.5098	-0.0551	0.9413	0.0352	-0.1908	0.0877	-0.3494	0.4689	-0.2008	-0.2429	-26.3524	64.301	-13.0463
47	1.0586	0.7093	0.0282	1.0601	-0.7726	4.644	0.1926	-1.0759	0.0206	0.6566	0.1116	0.2518	0.0423	0.3065	-0.3042	0.0549	-0.0556	0.0537	0.2071	-0.2223	-0.2428	-59.8293	73.3933	6.6343
48	3.6129	0.3298	-1.3079	1.2904	-0.0871	2.1913	0.0009	0.0987	0.0277	-0.3656	-0.0088	-0.645	-0.0928	0.7011	0.0079	-0.2277	-0.0761	-0.005	0.4007	-0.2287	0.0431	-5.0639	72.8359	-49.6978

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	2 - 40	2 - 40
2	X-RAY DIFFRACTION	1	A	A	325 - 502	325 - 502
3	X-RAY DIFFRACTION	2	A	A	41 - 133	41 - 133
4	X-RAY DIFFRACTION	3	A	A	134 - 180	134 - 180
5	X-RAY DIFFRACTION	3	A	A	272 - 324	272 - 324
6	X-RAY DIFFRACTION	4	A	A	181 - 271	181 - 271
7	X-RAY DIFFRACTION	5	A	A	570 - 672	570 - 672
8	X-RAY DIFFRACTION	6	A	A	673 - 723	673 - 723
9	X-RAY DIFFRACTION	6	A	A	812 - 859	812 - 859
10	X-RAY DIFFRACTION	7	A	A	724 - 811	724 - 811
11	X-RAY DIFFRACTION	8	A	A	503 - 569	503 - 569
12	X-RAY DIFFRACTION	8	A	A	860 - 1033	860 - 1033
13	X-RAY DIFFRACTION	9	B	B	2 - 40	2 - 40
14	X-RAY DIFFRACTION	9	B	B	325 - 502	325 - 502
15	X-RAY DIFFRACTION	10	B	B	41 - 133	41 - 133
16	X-RAY DIFFRACTION	11	B	B	134 - 180	134 - 180
17	X-RAY DIFFRACTION	11	B	B	272 - 324	272 - 324
18	X-RAY DIFFRACTION	12	B	B	181 - 271	181 - 271
19	X-RAY DIFFRACTION	13	B	B	570 - 672	570 - 672
20	X-RAY DIFFRACTION	14	B	B	673 - 723	673 - 723
21	X-RAY DIFFRACTION	14	B	B	812 - 859	812 - 859
22	X-RAY DIFFRACTION	15	B	B	724 - 811	724 - 811
23	X-RAY DIFFRACTION	16	B	B	503 - 569	503 - 569
24	X-RAY DIFFRACTION	16	B	B	860 - 1033	860 - 1033
25	X-RAY DIFFRACTION	17	C	C	2 - 40	2 - 40
26	X-RAY DIFFRACTION	17	C	C	325 - 502	325 - 502
27	X-RAY DIFFRACTION	18	C	C	41 - 133	41 - 133
28	X-RAY DIFFRACTION	19	C	C	134 - 180	134 - 180
29	X-RAY DIFFRACTION	19	C	C	272 - 324	272 - 324
30	X-RAY DIFFRACTION	20	C	C	181 - 271	181 - 271
31	X-RAY DIFFRACTION	21	C	C	570 - 672	570 - 672
32	X-RAY DIFFRACTION	22	C	C	673 - 723	673 - 723
33	X-RAY DIFFRACTION	22	C	C	812 - 859	812 - 859
34	X-RAY DIFFRACTION	23	C	C	724 - 811	724 - 811
35	X-RAY DIFFRACTION	24	C	C	503 - 569	503 - 569
36	X-RAY DIFFRACTION	24	C	C	860 - 1033	860 - 1033
37	X-RAY DIFFRACTION	25	D	D	2 - 40	2 - 40
38	X-RAY DIFFRACTION	25	D	D	325 - 502	325 - 502
39	X-RAY DIFFRACTION	26	D	D	41 - 133	41 - 133
40	X-RAY DIFFRACTION	27	D	D	134 - 180	134 - 180
41	X-RAY DIFFRACTION	27	D	D	272 - 324	272 - 324
42	X-RAY DIFFRACTION	28	D	D	181 - 271	181 - 271
43	X-RAY DIFFRACTION	29	D	D	570 - 672	570 - 672
44	X-RAY DIFFRACTION	30	D	D	673 - 723	673 - 723
45	X-RAY DIFFRACTION	30	D	D	812 - 859	812 - 859
46	X-RAY DIFFRACTION	31	D	D	724 - 811	724 - 811
47	X-RAY DIFFRACTION	32	D	D	503 - 569	503 - 569
48	X-RAY DIFFRACTION	32	D	D	860 - 1033	860 - 1033
49	X-RAY DIFFRACTION	33	E	E	2 - 40	2 - 40
50	X-RAY DIFFRACTION	33	E	E	325 - 502	325 - 502
51	X-RAY DIFFRACTION	34	E	E	41 - 133	41 - 133
52	X-RAY DIFFRACTION	35	E	E	134 - 180	134 - 180
53	X-RAY DIFFRACTION	35	E	E	272 - 324	272 - 324
54	X-RAY DIFFRACTION	36	E	E	181 - 271	181 - 271
55	X-RAY DIFFRACTION	37	E	E	570 - 672	570 - 672
56	X-RAY DIFFRACTION	38	E	E	673 - 723	673 - 723
57	X-RAY DIFFRACTION	38	E	E	812 - 859	812 - 859
58	X-RAY DIFFRACTION	39	E	E	724 - 811	724 - 811
59	X-RAY DIFFRACTION	40	E	E	503 - 569	503 - 569
60	X-RAY DIFFRACTION	40	E	E	860 - 1033	860 - 1033
61	X-RAY DIFFRACTION	41	F	F	2 - 40	2 - 40
62	X-RAY DIFFRACTION	41	F	F	325 - 502	325 - 502
63	X-RAY DIFFRACTION	42	F	F	41 - 133	41 - 133
64	X-RAY DIFFRACTION	43	F	F	134 - 180	134 - 180
65	X-RAY DIFFRACTION	43	F	F	272 - 324	272 - 324
66	X-RAY DIFFRACTION	44	F	F	181 - 271	181 - 271
67	X-RAY DIFFRACTION	45	F	F	570 - 672	570 - 672
68	X-RAY DIFFRACTION	46	F	F	673 - 723	673 - 723
69	X-RAY DIFFRACTION	46	F	F	812 - 859	812 - 859
70	X-RAY DIFFRACTION	47	F	F	724 - 811	724 - 811
71	X-RAY DIFFRACTION	48	F	F	503 - 569	503 - 569
72	X-RAY DIFFRACTION	48	F	F	860 - 1033	860 - 1033

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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