PDB-6yca: Crystal structure of Eis1 from Mycobacterium abscessus

ID or keywords:

Entry

Database: PDB / ID: 6yca

Title

Crystal structure of Eis1 from Mycobacterium abscessus

Components

Uncharacterized N-acetyltransferase D2E76_00625

Keywords

TRANSFERASE / GCN5-related N-acetyltransferase / Eis

Function / homology

Function and homology information

aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / host cell cytoplasmic vesicle / extracellular region
Similarity search - Function

Biological species

Mycobacteroides abscessus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Blaise, M. / Ung, K.L.

Citation

Journal: Proteins / Year: 2021
Title: Structural analysis of the N-acetyltransferase Eis1 from Mycobacterium abscessus reveals the molecular determinants of its incapacity to modify aminoglycosides.
Authors: Ung, K.L. / Kremer, L. / Blaise, M.

History

Deposition	Mar 18, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 9, 2020	Provider: repository / Type: Initial release
Revision 1.1	Sep 16, 2020	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Dec 21, 2022	Group: Database references / Category: citation / citation_author / database_2 Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6yca.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb6yca.ent.gz	745 KB	Display	PDB format
PDBx/mmJSON format	6yca.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yc/6yca ftp://data.pdbj.org/pub/pdb/validation_reports/yc/6yca	HTTPS FTP

-
Related structure data

Related structure data	6rftS S: Starting model for refinement
Similar structure data	6vur-1 6vv1-1 3ryo-1 6vuy-1 6p3t-1 6vuu-1 5ec4-1 6vuw-1 6p3v-1 6vv3-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (10) #97 - Jan 2008 Circadian Clock Proteins similarity (3)

Deposited unit

A: Uncharacterized N-acetyltransferase D2E76_00625

B: Uncharacterized N-acetyltransferase D2E76_00625

C: Uncharacterized N-acetyltransferase D2E76_00625

D: Uncharacterized N-acetyltransferase D2E76_00625

E: Uncharacterized N-acetyltransferase D2E76_00625

F: Uncharacterized N-acetyltransferase D2E76_00625

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	118.390, 150.690, 166.740
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1
5	1
6	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	THR	THR	PRO	PRO	(chain 'A' and (resid 24 through 50 or resid 59 through 73 or resid 75 through 415 or resid 501))	A	A	24 - 50	24 - 50
1	2	GLU	GLU	GLN	GLN	(chain 'A' and (resid 24 through 50 or resid 59 through 73 or resid 75 through 415 or resid 501))	A	A	59 - 72	59 - 72
1	3	LEU	LEU	PHE	PHE	(chain 'A' and (resid 24 through 50 or resid 59 through 73 or resid 75 through 415 or resid 501))	A	A	75 - 415	75 - 415
1	4	ACO	ACO	ACO	ACO	(chain 'A' and (resid 24 through 50 or resid 59 through 73 or resid 75 through 415 or resid 501))	A	G	501
2	5	THR	THR	PRO	PRO	(chain 'B' and (resid 24 through 50 or resid 59 through 73 or resid 75 through 415 or resid 501))	B	B	24 - 50	24 - 50
2	6	GLU	GLU	GLN	GLN	(chain 'B' and (resid 24 through 50 or resid 59 through 73 or resid 75 through 415 or resid 501))	B	B	59 - 72	59 - 72
2	7	LEU	LEU	PHE	PHE	(chain 'B' and (resid 24 through 50 or resid 59 through 73 or resid 75 through 415 or resid 501))	B	B	75 - 415	75 - 415
2	8	ACO	ACO	ACO	ACO	(chain 'B' and (resid 24 through 50 or resid 59 through 73 or resid 75 through 415 or resid 501))	B	M	501
3	9	THR	THR	PRO	PRO	(chain 'C' and (resid 24 through 50 or resid 59 through 73 or resid 75 through 415 or resid 501))	C	C	24 - 50	24 - 50
3	10	GLU	GLU	GLN	GLN	(chain 'C' and (resid 24 through 50 or resid 59 through 73 or resid 75 through 415 or resid 501))	C	C	59 - 72	59 - 72
3	11	LEU	LEU	PHE	PHE	(chain 'C' and (resid 24 through 50 or resid 59 through 73 or resid 75 through 415 or resid 501))	C	C	75 - 415	75 - 415
3	12	ACO	ACO	ACO	ACO	(chain 'C' and (resid 24 through 50 or resid 59 through 73 or resid 75 through 415 or resid 501))	C	T	501
4	13	THR	THR	PRO	PRO	(chain 'D' and (resid 24 through 73 or resid 75 through 415 or resid 501))	D	D	24 - 50	24 - 50
4	14	GLU	GLU	GLN	GLN	(chain 'D' and (resid 24 through 73 or resid 75 through 415 or resid 501))	D	D	59 - 72	59 - 72
4	15	LEU	LEU	PHE	PHE	(chain 'D' and (resid 24 through 73 or resid 75 through 415 or resid 501))	D	D	75 - 415	75 - 415
4	16	ACO	ACO	ACO	ACO	(chain 'D' and (resid 24 through 73 or resid 75 through 415 or resid 501))	D	Z	501
5	17	THR	THR	PRO	PRO	(chain 'E' and (resid 24 through 50 or resid 59 through 73 or resid 75 through 415 or resid 501))	E	E	24 - 50	24 - 50
5	18	GLU	GLU	GLN	GLN	(chain 'E' and (resid 24 through 50 or resid 59 through 73 or resid 75 through 415 or resid 501))	E	E	59 - 72	59 - 72
5	19	LEU	LEU	PHE	PHE	(chain 'E' and (resid 24 through 50 or resid 59 through 73 or resid 75 through 415 or resid 501))	E	E	75 - 415	75 - 415
5	20	ACO	ACO	ACO	ACO	(chain 'E' and (resid 24 through 50 or resid 59 through 73 or resid 75 through 415 or resid 501))	E	CA	501
6	21	THR	THR	PRO	PRO	(chain 'F' and (resid 24 through 50 or resid 59 through 73 or resid 75 through 415 or resid 501))	F	F	24 - 50	24 - 50
6	22	GLU	GLU	GLN	GLN	(chain 'F' and (resid 24 through 50 or resid 59 through 73 or resid 75 through 415 or resid 501))	F	F	59 - 72	59 - 72
6	23	LEU	LEU	PHE	PHE	(chain 'F' and (resid 24 through 50 or resid 59 through 73 or resid 75 through 415 or resid 501))	F	F	75 - 415	75 - 415
6	24	ACO	ACO	ACO	ACO	(chain 'F' and (resid 24 through 50 or resid 59 through 73 or resid 75 through 415 or resid 501))	F	GA	501

#1: Protein	Uncharacterized N-acetyltransferase D2E76_00625 Mass: 44899.383 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: D2E76_00625 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: A0A418LDP6, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical	ChemComp-ACO / ACETYL COENZYME A Mass: 809.571 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₃H₃₈N₇O₁₇P₃S / Feature type*: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO₄
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.75 Å³/Da / Density % sol: 55 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.8 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5 and 1% PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 1, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.9→50 Å / Num. obs: 65973 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / B_iso Wilson estimate: 38.36 Å² / CC_1/2: 0.98 / R_rim(I) all: 0.19 / Net I/σ(I): 9.3
Reflection shell	Resolution: 2.9→3 Å / Num. unique obs: 6337 / CC_1/2: 0.74 / R_rim(I) all: 0.78 / % possible all: 99.7

-
Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
PHENIX	1.17.1_3660	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6RFT

6rft

Resolution: 2.9→48.27 Å / SU ML: 0.3462 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.6442

	R_factor	Num. reflection	% reflection
R_free	0.2485	3299	5 %
R_work	0.2076	-	-
obs	0.2097	65964	98.84 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 34.05 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→48.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17879	0	421	0	18300

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0035	18715
X-RAY DIFFRACTION	f_angle_d	0.7223	25656
X-RAY DIFFRACTION	f_chiral_restr	0.0701	2915
X-RAY DIFFRACTION	f_plane_restr	0.0045	3290
X-RAY DIFFRACTION	f_dihedral_angle_d	14.7879	6668

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 (%)
2.9-2.94	0.3337	136	0.28	2591	X-RAY DIFFRACTION	99.71
2.94-2.99	0.3046	137	0.2697	2603	X-RAY DIFFRACTION	99.6
2.99-3.03	0.3497	136	0.2758	2582	X-RAY DIFFRACTION	99.31
3.03-3.08	0.3235	138	0.2743	2613	X-RAY DIFFRACTION	99.67
3.08-3.13	0.3093	137	0.2697	2608	X-RAY DIFFRACTION	99.67
3.13-3.19	0.3256	136	0.2566	2586	X-RAY DIFFRACTION	99.34
3.19-3.25	0.3207	137	0.2531	2599	X-RAY DIFFRACTION	99.6
3.25-3.32	0.3187	135	0.2525	2566	X-RAY DIFFRACTION	99.37
3.32-3.39	0.3146	138	0.2476	2619	X-RAY DIFFRACTION	99.32
3.39-3.47	0.2544	137	0.2225	2604	X-RAY DIFFRACTION	98.99
3.47-3.56	0.279	136	0.2256	2585	X-RAY DIFFRACTION	99.49
3.56-3.65	0.2744	137	0.2384	2608	X-RAY DIFFRACTION	99.1
3.65-3.76	0.2689	137	0.2454	2593	X-RAY DIFFRACTION	98.7
3.76-3.88	0.2073	137	0.1997	2606	X-RAY DIFFRACTION	99.1
3.88-4.02	0.2167	136	0.1908	2596	X-RAY DIFFRACTION	98.88
4.02-4.18	0.235	136	0.1751	2576	X-RAY DIFFRACTION	97.2
4.18-4.37	0.1977	137	0.169	2591	X-RAY DIFFRACTION	98.52
4.37-4.6	0.2273	138	0.1685	2634	X-RAY DIFFRACTION	99.32
4.6-4.89	0.1948	139	0.1624	2638	X-RAY DIFFRACTION	99.39
4.89-5.27	0.2021	138	0.1637	2620	X-RAY DIFFRACTION	98.75
5.27-5.8	0.2367	139	0.1834	2644	X-RAY DIFFRACTION	98.51
5.8-6.63	0.2298	139	0.1926	2644	X-RAY DIFFRACTION	98.17
6.63-8.35	0.1938	139	0.1766	2635	X-RAY DIFFRACTION	97.06
8.35-48.27	0.1924	144	0.1699	2724	X-RAY DIFFRACTION	95.95

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	3.17489339279	0.00585059302539	-2.33713760501	1.47100703149	-0.903927206166	3.58132737128	-0.264713009684	-0.370860355554	-0.543053878442	0.148014671711	0.0577322623138	0.0631577960687	0.361539561254	0.115771189188	0.173668381154	0.267961686713	0.0787779120422	-0.0530845066842	0.282527726316	0.0380207826944	0.300969939647	96.7762127894	62.1097352252	62.0840455619
2	1.0992881167	-0.197444605084	0.929361840697	1.44803288674	0.36313986454	1.88641691098	-0.00818761806562	-0.0116936769351	-0.0518753456221	-0.0365917352901	0.059793327721	-0.226843989747	-0.0156341947106	0.162014844577	-0.0442230093696	0.15630409568	0.00386138516809	0.0801862357485	0.210994893521	0.0153158989403	0.248597761369	96.916417792	74.6462981724	41.8703730288
3	5.60480791977	2.97814700327	2.73762409512	6.14696779838	2.96175656971	6.86184433278	0.114314119767	0.151499658837	-0.534971969165	-0.242483722696	-0.629033004015	0.510947883666	0.7744090479	-0.00718851842286	0.520119902667	0.364260262894	0.113224614431	0.020968538366	0.248664276208	-0.111147585582	0.375508410372	68.941123921	56.4338038631	19.8698179306
4	4.82361165819	-0.134123657546	0.377471193362	1.42572328639	0.55169969509	1.35305748523	0.0778712336183	0.175977071672	-0.333119162777	-0.160848261403	-0.0246412272413	0.00981019615267	0.312988215379	0.0220132257262	-0.0452022222645	0.328866569061	0.0088171150592	-0.0376988635104	0.170284975538	-0.0320441866308	0.170905131945	61.3596071536	64.8538515454	17.4252498282
5	1.51653056663	-0.416317750039	-1.40377130028	0.864152361362	-0.788320960873	3.02718237829	-0.0362729357486	-0.0264149553583	0.00527283970155	0.162149601031	0.0268827753819	0.240917893551	0.107748666673	-0.0583163891032	0.00793481424374	0.261313650539	-0.070844635358	-0.0371589402131	0.175044435634	-0.0318985619899	0.278860312942	42.7197826466	71.2765733924	37.1427102352
6	0.893164887306	0.0640521581982	-1.33348752426	0.469186879553	1.15011320363	5.29514920937	-0.0785863922113	-0.0968157692739	0.0227084881601	-0.108249096108	0.0656198813579	-0.0565437643477	0.775099046952	0.449999412995	-0.00773138551803	0.39623289899	0.0537621391454	-0.0196450122447	0.169106092463	-0.00441674508501	0.410627051005	50.2203223694	60.6146651501	38.694801867
7	7.94571514798	-2.00309329979	4.88202264781	2.18408327496	-1.31093783128	5.46415654694	-0.101463252497	0.0200399891924	0.668300791155	0.428741119483	-0.293438456986	-0.158258823088	0.480559616665	0.194873986884	0.388838286159	0.406733651278	-0.0472926890962	0.0605261270587	0.138700913118	-0.0166172008399	0.323132269444	49.5136296424	70.9112205319	47.1773209709
8	1.57071207225	0.687256060202	0.0759232873138	4.39600619606	-1.87069890581	7.60922177929	0.00970531776848	-0.0740027417259	0.0693055035227	0.011577253327	-0.270944321015	0.21378796464	0.140036206274	-0.195313702025	0.259133248837	0.118117699212	-0.0169273500159	0.00156267815573	0.187674145767	-0.0214564592328	0.21000028108	41.1957792844	78.0479922805	42.4844447559
9	1.38740300815	-0.317107896197	-1.30313478043	0.433793928827	0.397015078649	3.70681145124	0.106149786984	0.296538735052	0.032522794718	-0.216890457536	0.0274993995276	0.102177629093	0.0290971657592	-0.0320606446935	-0.109879020856	0.230989746744	-0.032343238844	-0.072367460957	0.177229234278	0.00902108130954	0.258454248806	47.447126361	81.2672362349	11.1866454875
10	4.80137356924	-0.528701038011	-0.318312548494	2.49204882663	0.556226377343	3.16144281146	0.135533422767	0.259731002185	0.502454418512	-0.154889215385	0.0772522304639	0.407080634046	-0.384734494088	-0.376011417378	-0.214896064337	0.259213381548	-0.00719412571039	0.0118132559321	0.125500222546	-0.0928651584868	0.233851624129	45.7279075682	84.8661065304	16.0064735554
11	3.30912140698	1.13978561393	-2.11058041829	1.49941877203	-0.145223190152	3.40272705151	0.198328602703	0.0659866933922	0.443423280762	0.175053382517	0.069686600306	-0.175449141639	-0.686682581802	0.339480482252	-0.296228365482	0.431748139382	-0.0412991651721	-0.075559390748	0.239916731383	-0.0140758867633	0.277525760163	79.8860823179	110.453427267	79.9901134523
12	1.12006015938	-0.71308247045	1.32245726894	0.84618370126	-0.416539586479	2.41236379086	-0.0309595334094	0.0450901864	0.0285592588855	0.036712386102	0.00520930251598	-0.0530383740895	-0.197733191467	0.0699636442996	0.0291773694621	0.181035371091	-0.0436173216563	0.0290537112296	0.149093111246	-0.000358594319517	0.202715540719	59.0934193398	98.5608607587	79.0770220259
13	4.88824430517	-1.01767289041	0.759325970075	0.865336743064	-0.752810521034	1.95455685466	-0.0162972808345	0.211611064164	0.41721708632	-0.204004760203	-0.0387011390288	-0.124469615585	-0.233739420003	0.00986162955688	0.0424938324535	0.293193778025	-0.0222156172294	0.0365611197641	0.139598383342	-0.00323333805095	0.219449280877	88.486574662	110.120815663	24.7851928952
14	0.613404348907	-0.313885552459	-0.752059725343	1.43039301393	0.93021777549	2.9747844806	0.0850830328319	-0.0665766629439	0.136948169859	-0.014789529536	0.0985480414131	-0.242245999241	-0.155773048692	0.234345249277	-0.182455946663	0.156350134998	-0.0434242187762	-0.0354399334665	0.180351965458	0.0127571517638	0.303849213971	97.6235308127	97.8512225723	42.9496569358
15	2.28089969719	-1.06833079308	1.99264597713	8.97279046359	-1.66881160418	3.62509233345	-0.289847945911	-0.237440636406	0.766037378229	0.0373036384377	-0.0498692546897	0.17170990493	-0.617878565887	-0.245107642556	0.360436553289	0.26978755153	0.0363413415768	-0.0850811123552	0.319383951397	-0.108719774182	0.365323995372	37.4299495882	117.487086021	51.5788044532
16	1.79945199213	-0.847725205771	0.872203554667	1.46744341827	0.0658037077693	5.51125167521	-0.100374330342	-0.0372263649929	0.15036433776	0.0731211643693	0.0394518446532	0.219183356825	-0.438930592461	-0.179539271567	0.0503471967004	0.16881822159	0.00957768898826	-0.0440955443321	0.187358947207	-0.0269650520728	0.294993359522	35.3725225229	109.302646262	43.2249440977
17	2.64439588833	0.839343771545	-1.49256089697	1.06375075533	-0.377061431229	1.32880783709	-0.00943055265398	0.0589884807758	0.183565602624	-0.134183301864	0.0980421110231	-0.0977299138801	-0.0781429482638	-0.00614462268568	-0.0867774620834	0.313281835202	0.0325121714416	-0.0843360940189	0.159619339225	0.00608041794756	0.249351920183	56.3905836739	106.723941692	27.8018305222
18	7.3395788764	1.00293171835	3.72896880791	3.40282501439	2.27258325218	5.6099252508	0.101454991827	0.0815883894571	0.101817659462	0.32192218964	-0.0308741149796	-0.0320030679086	0.241135755322	0.205777699548	-0.0582115129258	0.257997796754	-0.0222379487697	0.0207505034962	0.117326432987	0.064135468171	0.171386452361	65.229391828	101.535552824	28.5343856793
19	6.78795019246	-3.77266864209	-2.00883969141	2.30220030814	0.829821777495	0.976274711664	-0.086122271234	-0.0682055562217	0.42380077925	0.0503736636518	0.0993284063851	-0.166201078445	0.0244511162981	0.0727132184899	0.0150592392211	0.228941867064	0.00376758123665	-0.0582367822787	0.248336182442	-0.0533905270258	0.188603945252	50.0643977012	93.5242916371	29.6428354707
20	2.52176832703	0.154074959867	-0.0464901688679	2.23540938043	0.237877057604	2.20947470665	-0.0940955466452	0.433476585931	-0.136624129832	-0.440290348462	0.0321427204146	0.686401594383	0.104465189348	-0.528278056821	0.0776303123197	0.274635682533	-0.0412179603367	-0.114499876063	0.329495299658	-0.0266890080075	0.349580027098	27.8284061539	92.4896199412	27.0748260604
21	1.3202872623	0.497166308858	1.97615849836	1.3200336821	0.856121144958	4.46028364021	0.088692173868	0.0574177704885	-0.245137471261	0.131759848614	-0.0637244247832	0.0531173025159	0.40516152622	-0.125815306275	-0.0417233831314	0.22647287292	-0.00739547596361	0.0967686386759	0.188450223533	-0.0125690366287	0.277682560895	41.4195360766	63.6397628625	69.4016246247
22	3.22010248814	-0.229926559289	-1.31898442195	0.907008261094	0.371402151692	1.59397771543	-0.216322848049	0.102632040672	-0.220218661112	0.0268636894162	0.0561105356002	-0.198643140155	0.313333111976	-0.049853034387	0.127151094028	0.289300887292	-0.0162636773753	-0.0377170412995	0.161431171014	-0.00786617978971	0.21500400682	70.9537491615	69.1239172214	73.1484548499
23	3.90121236794	0.801177727462	-0.520149357563	1.73564450063	-0.430821172671	0.966001684141	-0.149591594428	-0.296516979592	0.266190645467	0.482841222805	0.104380035296	0.229352790206	-0.00426929335605	-0.109614302984	0.0434384605445	0.387032051595	0.0242467318713	0.0351518412898	0.193948937898	-0.025911801627	0.194932895282	48.2161227708	81.8440420873	85.5781859429

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 24 through 147 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 148 through 415 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 24 through 46 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 47 through 147 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 148 through 203 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 204 through 228 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 229 through 258 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 259 through 295 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 296 through 384 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 385 through 415 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 23 through 147 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 148 through 415 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 23 through 148 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 149 through 415 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 23 through 46 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 47 through 147 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 148 through 228 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 229 through 280 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 281 through 314 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 315 through 415 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 23 through 147 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 148 through 280 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 281 through 415 )

-
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