PDB-4z3y: Active site complex BamBC of Benzoyl Coenzyme A reductase in comp...

ID or keywords:

Entry

Database: PDB / ID: 4z3y

Title

Active site complex BamBC of Benzoyl Coenzyme A reductase in complex with Benzoyl-CoA

Components

Benzoyl-CoA reductase, putative
Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein

Keywords

OXIDOREDUCTASE / aromatics / reductase / Benzoyl-CoA / anaerobic

Function / homology

Function and homology information

oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function

Biological species

Geobacter metallireducens GS-15 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.359 Å

Authors

Weinert, T. / Kung, J.W. / Weidenweber, S. / Huwiler, S.G. / Boll, M. / Ermler, U.

Citation

Journal: Nat.Chem.Biol. / Year: 2015
Title: Structural basis of enzymatic benzene ring reduction.
Authors: Weinert, T. / Huwiler, S.G. / Kung, J.W. / Weidenweber, S. / Hellwig, P. / Stark, H.J. / Biskup, T. / Weber, S. / Cotelesage, J.J. / George, G.N. / Ermler, U. / Boll, M.

History

Deposition	Apr 1, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jul 1, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jul 8, 2015	Group: Database references
Revision 1.2	Jan 10, 2024	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_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4z3y.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb4z3y.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	4z3y.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4z3y_validation.pdf.gz	4.4 MB	Display	wwPDB validaton report
Full document	4z3y_full_validation.pdf.gz	4.5 MB	Display
Data in XML	4z3y_validation.xml.gz	114.3 KB	Display
Data in CIF	4z3y_validation.cif.gz	148.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z3/4z3y ftp://data.pdbj.org/pub/pdb/validation_reports/z3/4z3y	HTTPS FTP

-
Related structure data

Related structure data	4z3wC 4z3xC 4z3zC 4z40SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4z3w-d 4z3x-d 4z40-d 4z3z-d 5dgy-1 7m7w-d 4r83-d 31193 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	#117 - Sep 2009 Xanthine Oxidoreductase similarity (1) #235 - Jul 2019 AMPA Receptor similarity (1) #220 - Apr 2018 Dehalogenases similarity (2) #111 - Mar 2009 Hydrogenase similarity (2) #144 - Dec 2011 Complex I similarity (2) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (2) #154 - Oct 2012 Citric Acid Cycle similarity (2) #22 - Oct 2001 Photosystem I similarity (2) #66 - Jun 2005 Carotenoid Oxygenase similarity (2) #137 - May 2011 Cytochrome bc1 similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (2)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#117 - Sep 2009
Xanthine Oxidoreductase
similarity (1)
#235 - Jul 2019
AMPA Receptor
similarity (1)
#220 - Apr 2018
Dehalogenases
similarity (2)
#111 - Mar 2009
Hydrogenase
similarity (2)
#144 - Dec 2011
Complex I
similarity (2)
#244 - Apr 2020
Photosynthetic Supercomplexes
similarity (2)
#154 - Oct 2012
Citric Acid Cycle
similarity (2)
#22 - Oct 2001
Photosystem I
similarity (2)
#66 - Jun 2005
Carotenoid Oxygenase
similarity (2)
#137 - May 2011
Cytochrome bc1
similarity (1)
#191 - Nov 2015
Glutamate-gated Chloride Receptors
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (2)

Deposited unit

A: Benzoyl-CoA reductase, putative

B: Benzoyl-CoA reductase, putative

C: Benzoyl-CoA reductase, putative

D: Benzoyl-CoA reductase, putative

E: Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein

F: Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein

G: Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein

H: Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein

hetero molecules

389 kDa, 8 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)	125.767, 116.256, 143.973
Angle α, β, γ (deg.)	90.00, 110.43, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain 'A' and (resseq 1:653 )
2	1	1	chain 'B' and (resseq 1:653 )

-
Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein	Benzoyl-CoA reductase, putative Mass: 73895.477 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacter metallireducens GS-15 (bacteria) Gene: bamB-1, Gmet_2087 / Production host: Geobacter metallireducens (bacteria) / Strain (production host): GS-15 / References: UniProt: Q39TV8
#2: Protein	Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein Mass: 20133.945 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacter metallireducens GS-15 (bacteria) Gene: bamC-1, Gmet_2086 / Production host: Geobacter metallireducens (bacteria) / Strain (production host): GS-15 / References: UniProt: Q39TV9

#1: Protein

Benzoyl-CoA reductase, putative

Mass: 73895.477 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Geobacter metallireducens GS-15 (bacteria)
Gene: bamB-1, Gmet_2087 / Production host:

Geobacter metallireducens (bacteria) / Strain (production host): GS-15 / References: UniProt: Q39TV8

#2: Protein

Iron-sulfur cluster-binding oxidoreductase, putative benzoyl-CoA reductase electron transfer protein

Mass: 20133.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Geobacter metallireducens GS-15 (bacteria)
Gene: bamC-1, Gmet_2086 / Production host:

Geobacter metallireducens (bacteria) / Strain (production host): GS-15 / References: UniProt: Q39TV9

-
Non-polymers , 6 types, 40 molecules

#3: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe₄S₄
#4: Chemical	ChemComp-MTE / PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER Mass: 395.352 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₆PS₂
#5: Chemical	ChemComp-W / TUNGSTEN ION Mass: 183.840 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: W
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical	ChemComp-UNL / UNKNOWN LIGAND Num. of mol.: 4 / Source method: obtained synthetically
#8: Chemical	ChemComp-BYC / benzoyl coenzyme A Mass: 871.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₈H₄₀N₇O₁₇P₃S

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.62 Å³/Da / Density % sol: 53.1 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 7 % (w/v) PEG 4000 0.2 M LiCl 0.1 M Tris pH 8.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.35→79.85 Å / Num. all: 159187 / Num. obs: 150908 / % possible obs: 94.8 % / Redundancy: 2.9 % / R_sym value: 0.173 / Net I/σ(I): 5.48
Reflection shell	Resolution: 2.35→2.49 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.136 / Mean I/σ(I) obs: 0.85 / % possible all: 91.5

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4Z40

4z40

Resolution: 2.359→79.804 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.82 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2746	1979	1.31 %
R_work	0.2415	-	-
obs	0.2419	150665	94.31 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.359→79.804 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25805	0	556	0	26361

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	27160
X-RAY DIFFRACTION	f_angle_d	0.706	36782
X-RAY DIFFRACTION	f_dihedral_angle_d	13.598	10334
X-RAY DIFFRACTION	f_chiral_restr	0.025	3914
X-RAY DIFFRACTION	f_plane_restr	0.003	4797

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	5186	X-RAY DIFFRACTION	POSITIONAL
1	2	B	5186	X-RAY DIFFRACTION	POSITIONAL	0.002

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 (%)
2.3588-2.4178	0.4755	120	0.3979	8907	X-RAY DIFFRACTION	79
2.4178-2.4832	0.404	152	0.3727	10699	X-RAY DIFFRACTION	96
2.4832-2.5563	0.3945	137	0.3493	10759	X-RAY DIFFRACTION	96
2.5563-2.6388	0.351	145	0.3294	10788	X-RAY DIFFRACTION	96
2.6388-2.7331	0.3678	138	0.3258	10749	X-RAY DIFFRACTION	96
2.7331-2.8425	0.3635	144	0.3121	10724	X-RAY DIFFRACTION	95
2.8425-2.9719	0.3266	141	0.2902	10690	X-RAY DIFFRACTION	95
2.9719-3.1286	0.2911	135	0.2737	10741	X-RAY DIFFRACTION	96
3.1286-3.3246	0.3152	150	0.2713	10744	X-RAY DIFFRACTION	96
3.3246-3.5813	0.2913	137	0.2616	10694	X-RAY DIFFRACTION	95
3.5813-3.9417	0.2794	143	0.2244	10667	X-RAY DIFFRACTION	95
3.9417-4.5121	0.2188	148	0.1977	10860	X-RAY DIFFRACTION	96
4.5121-5.6845	0.223	138	0.1929	10808	X-RAY DIFFRACTION	95
5.6845-79.85	0.2008	151	0.1783	10856	X-RAY DIFFRACTION	94

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	2.0053	0.3902	-1.0569	0.7119	-0.0964	1.5889	0.0899	-0.0942	-0.0475	-0.2389	-0.0934	-0.1438	-0.1322	0.0789	0.0079	0.5515	0.0226	0.2372	0.3258	0.0086	0.6233	44.8222	27.9399	11.1037
2	4.7762	0.5243	-1.3823	2.1223	0.017	3.3086	-0.0906	0.8013	-0.3216	-0.9899	0.0644	0.003	0.1203	-0.344	0.0906	0.9251	0.0712	0.1685	0.3649	0.0068	0.4303	38.4986	25.7751	-14.1016
3	1.6676	0.6982	-0.9714	0.9953	-0.4771	1.3906	0.1402	-0.2895	0.0105	-0.2875	-0.1343	-0.5381	-0.182	0.3766	-0.0172	0.6223	-0.0263	0.3933	0.4669	0.0074	0.8923	65.0776	35.2599	4.3085
4	0.7788	0.147	-0.1928	0.4952	-0.3066	0.3668	0.9138	0.3729	1.3286	-0.6637	-0.2111	-0.2283	-1.1194	-0.2779	-0.2849	1.4206	0.5089	0.7991	0.6574	0.4551	1.2973	-6.9695	55.301	27.5974
5	0.8206	1.6108	-0.3019	3.6996	-1.2275	0.8928	-0.1847	0.395	0.2624	-0.6986	-0.0566	-0.1754	-0.2969	0.2204	0.361	2.0883	0.5374	0.7697	0.9611	0.6883	1.7118	-4.1998	76.3815	12.4863
6	0.1617	0.0548	0.1629	0.5944	-0.2115	0.2766	0.4517	0.64	0.6587	-0.6673	-0.0243	0.4795	-0.6186	-1.116	0.241	1.2298	1.0349	0.3698	1.5088	0.5491	1.2391	-28.4119	54.2995	20.3274
7	1.507	-0.0279	-0.3628	1.989	0.6708	1.4874	0.0166	-0.0832	-0.1213	-0.0694	-0.0413	-0.4624	0.0203	0.0969	0.0235	0.286	0.086	0.0738	0.3952	0.0533	0.5807	-31.7811	53.0214	78.8516
8	2.8781	0.0492	-0.0047	2.4429	-0.7919	1.1437	0.0338	-0.4434	0.0958	0.4901	0.1604	-0.3063	-0.0078	0.3281	-0.1866	0.2297	-0.001	-0.1399	0.3622	-0.0684	0.2828	-33.1306	71.7886	96.8165
9	1.4678	-0.328	0.0132	1.3658	0.6142	1.0171	-0.0357	-0.4072	-0.169	0.0727	0.2365	-0.7124	0.0991	0.544	-0.1331	0.3296	0.1052	0.0031	0.7532	0.022	0.9578	-10.9211	48.8648	86.758
10	2.0119	-0.1135	-0.8293	0.9402	-0.5107	2.1635	-0.1266	0.118	-0.4056	0.1716	-0.1056	0.3157	0.2315	-0.0302	0.1594	0.4343	-0.0557	0.1902	0.4427	-0.1756	0.6991	-86.4146	29.1741	90.3964
11	2.8326	0.7951	-1.2139	3.6957	-1.0899	3.581	-0.4519	-0.7822	-1.031	0.4783	-0.0451	-0.1365	0.4166	0.5961	0.449	0.6822	0.1931	0.2361	0.6765	0.2267	0.6948	-81.2728	22.9465	115.28
12	1.4512	0.197	-0.8623	1.1781	-0.6169	1.8925	-0.1079	0.2493	-0.3655	0.4089	0.0313	0.7851	0.0793	-0.455	0.0172	0.3823	-0.0413	0.1989	0.5709	-0.1453	0.8875	-105.9898	37.7624	97.7512
13	6.2299	6.1206	1.7052	6.0352	1.6006	1.0351	0.4539	-0.7388	0.6484	0.032	-0.1346	-0.1129	-0.5077	0.1845	-0.3405	0.8479	-0.1083	0.379	0.4286	-0.0742	0.8083	36.5263	39.4977	26.4852
14	2.6005	0.4091	-0.5695	2.0452	-0.4786	1.6623	0.2885	-0.3559	0.1056	0.146	-0.0781	0.1305	-0.2439	0.1144	-0.1969	0.4713	-0.0177	0.2264	0.4038	-0.007	0.6089	22.9632	29.1469	32.497
15	4.2291	3.3623	0.115	7.9148	-2.6294	3.1835	0.3303	-1.0848	-0.4015	0.7761	-0.198	0.3791	-0.2662	0.0607	-0.021	0.5192	-0.1509	0.2382	0.6763	0.0117	0.545	34.606	26.8388	42.3947
16	4.1776	-1.6707	-2.388	0.6771	0.949	1.3646	0.4272	-0.7641	0.7744	0.3048	-0.1431	-0.3376	-0.947	1.278	-0.3297	0.6881	-0.2458	0.2517	0.7369	-0.1234	0.82	40.4475	41.7102	38.8562
17	5.7855	-0.0901	-0.6843	2.3884	-0.7005	1.1819	0.5753	-1.2516	0.6958	0.6005	-0.0608	0.1721	-0.4722	0.3168	-0.603	0.6059	-0.2686	0.3876	0.6172	-0.2189	1.0169	29.8296	48.0466	38.6366
18	8.206	-0.5899	-1.4692	2.0053	1.309	8.9783	0.0416	-0.5901	0.2437	0.7277	-0.1976	0.8516	-0.3229	-0.8138	0.0993	0.5031	0.0204	0.1425	0.7424	0.0329	0.7341	3.3032	32.4028	57.4987
19	9.0615	3.2076	-6.8881	9.535	2.7957	8.4982	0.2066	-1.2219	-1.2732	0.5963	0.2824	-0.0201	0.7507	0.2578	-0.4318	0.765	0.0062	0.0958	0.708	0.136	0.7137	5.928	20.932	61.2236
20	0.8965	0.6744	-0.4588	1.0104	-1.1992	1.7029	0.6752	0.3649	0.8406	-0.5946	-0.1877	-0.3005	-0.4524	-0.0401	-0.3818	0.4616	0.0951	0.1662	0.374	0.0934	0.4311	3.8331	34.3501	33.7446
21	2.9419	0.3808	-1.0907	2.0379	-0.8775	2.628	0.6247	-0.4497	0.3958	0.1896	-0.0788	0.0957	-0.6647	0.3838	-0.5741	0.5796	-0.0453	0.3085	0.494	-0.0845	0.6776	17.5482	38.8713	37.7239
22	5.7808	0.8526	0.7848	2.4871	-0.1387	3.3362	0.2403	-0.4135	0.4855	0.4085	0.0319	-0.0008	0.6368	0.4823	-0.0976	0.3564	-0.0967	-0.0698	0.2997	-0.0011	0.1901	7.3713	32.2795	46.6804
23	0.0012	0.0077	0.0186	0.1211	0.1053	0.7859	0.1477	0.0198	-0.1795	-0.178	0.0625	0.2077	0.1586	-0.1356	0.1113	0.2965	0.1106	-0.2427	0.4126	0.1027	0.0276	0.1196	25.5774	33.5891
24	1.8053	0.189	0.6601	2.8284	-0.3414	8.1081	0.1138	-0.232	-0.4572	0.2092	-0.1091	-0.1462	0.514	0.5484	-0.0042	0.3749	-0.0196	0.0754	0.483	0.0423	0.5009	13.1852	19.9621	32.919
25	3.3925	2.0476	1.9409	8.0637	3.6115	6.3063	0.0277	0.0354	-0.2185	0.0471	-0.1512	-0.3411	0.3405	0.0187	0.0757	0.5476	-0.0542	0.1673	0.8411	-0.1459	0.4966	12.3591	28.6777	55.572
26	5.7783	-4.5915	-2.3245	7.0656	0.5986	2.135	0.1919	-1.7667	0.0946	1.0511	0.196	-0.2464	-0.3249	0.4423	-0.3797	0.7707	-0.1997	0.0045	1.0642	-0.2324	0.4505	7.4902	29.5094	66.6776
27	2.8936	-0.1117	-1.4359	0.9979	-0.27	1.7218	-0.0883	0.1882	-0.5489	0.0314	-0.0794	-0.0691	0.1918	-0.135	0.1408	0.2203	0.0449	-0.0598	0.2984	-0.0285	0.3364	-44.3037	34.3586	69.5461
28	3.5328	-0.7442	-0.9695	2.171	0.986	5.0654	0.1509	0.6952	0.0737	-0.3798	-0.1265	-0.1552	-0.1216	-0.5051	-0.0551	0.3658	0.0254	0.0993	0.4914	-0.0188	0.4734	-57.2441	40.944	65.9246
29	4.3774	-2.1827	2.2515	2.6512	1.293	5.0529	0.2883	1.0213	-0.4142	-0.769	0.2003	0.2957	0.3641	-0.0032	-0.3197	0.5056	0.0077	0.1259	0.5792	-0.1429	0.4992	-47.4614	34.8509	56.4421
30	4.463	-1.2713	-2.4877	2.697	1.244	1.5099	-0.0586	0.2653	-0.6761	-0.0251	-0.1875	-0.0882	0.6268	-0.0492	0.2056	0.4592	-0.014	0.1367	0.3681	-0.0048	0.6044	-41.6601	25.3992	68.2708
31	3.3727	-1.9274	-2.4943	1.7207	0.4143	3.5117	-0.2939	0.1164	-1.3588	0.2184	-0.116	0.2736	0.7869	-0.272	0.1079	0.3737	0.1219	0.029	0.1812	0.1454	0.6096	-49.7826	23.0932	75.8245
32	7.507	4.1962	-5.9405	5.9633	-5.1627	7.0965	0.1296	0.5461	-0.3853	-0.124	0.1056	0.4334	0.3648	-0.796	-0.2067	0.7277	-0.0052	-0.0685	1.2982	-0.1624	0.7838	-61.3385	19.0809	58.8786
33	7.5397	0.9061	-0.5252	7.6694	-2.7378	4.9129	0.1417	1.0124	-0.3974	-0.2062	-0.2725	0.0288	0.0374	0.0979	0.2029	0.6468	-0.1931	0.2285	1.2324	-0.3544	0.6821	-52.7865	33.4766	47.0092
34	0.3703	0.0067	-1.0191	0.4868	0.1127	2.8393	0.6052	2.1632	0.3343	-1.0676	-0.4886	-0.1298	-0.5009	-0.5627	-0.0746	1.9494	-0.3475	0.0852	2.057	0.1372	0.5962	-48.2746	35.8126	36.1994
35	2.6444	0.5129	1.2982	3.5039	0.1907	0.9319	-0.2735	0.513	-0.5744	-0.3517	0.0506	-0.1876	-0.083	-0.5534	0.1228	0.2422	-0.0395	0.0427	0.6472	-0.1924	0.3352	-76.327	39.4556	70.3114
36	4.1386	-1.0088	-0.4286	2.7884	0.2755	1.352	0.1853	0.8266	-0.2987	-0.213	-0.2526	0.0307	0.0576	-0.2121	0.0512	0.4333	-0.0766	0.1791	0.5245	-0.1766	0.6056	-63.8732	31.1734	69.7122
37	3.9998	-1.7629	0.0433	4.4736	4.7649	6.9519	0.0569	1.3875	-0.7675	-0.9931	-0.2586	-0.3859	0.0365	-0.2964	0.1163	0.4242	0.0005	0.0927	0.7179	-0.1971	0.3674	-75.3948	31.5859	59.5342
38	9.0568	0.0725	-3.1008	3.5714	-1.399	1.7056	0.6356	0.8599	0.3166	-0.4783	-0.1117	-0.2005	-0.1488	-0.609	-0.4456	0.5269	-0.0049	0.0314	0.6979	-0.0837	0.5178	-79.7077	46.2785	65.0724
39	2.7656	-1.1965	-2.1303	2.143	1.3439	2.5572	0.0604	0.7155	0.1074	-0.3118	0.1493	-0.6563	0.1555	-0.1213	-0.2324	0.3981	0.0244	-0.0916	0.8702	-0.1925	0.3883	-55.6079	43.2382	56.4859
40	4.3015	0.8752	-2.4038	0.2337	-0.5048	1.4393	0.2149	2.0732	-0.857	-0.8359	0.2459	-0.3448	0.6076	0.0539	-0.4172	1.4307	-0.1789	0.0628	1.8351	-0.6565	1.0944	-47.447	25.9945	40.3904

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and ((resid 1 through 349 ) or resid 1005 or resid 1003 or resid 1004 or resid 1002 or resid 1006 or resid 1008)
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 350 through 407 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 408 through 653 )
4	X-RAY DIFFRACTION	4	chain 'B' and ((resid 1 through 349 ) or resid 1004 or resid 1002 or resid 1006 or resid 1008)
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 350 through 407 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 408 through 653 )
7	X-RAY DIFFRACTION	7	chain 'C' and ((resid 1 through 349 ) or resid 1004 or resid 1002 or resid 1006 or resid 1008)
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 350 through 407 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 408 through 653 )
10	X-RAY DIFFRACTION	10	chain 'D' and ((resid 1 through 349 ) or resid 1004 or resid 1002 or resid 1006 or resid 1008)
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 350 through 407 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 408 through 652 )
13	X-RAY DIFFRACTION	13	chain 'E' and ((resid 6 through 57 ) or resid 1001)
14	X-RAY DIFFRACTION	14	chain 'E' and ((resid 58 through 104 ) or resid 1003)
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 105 through 114 )
16	X-RAY DIFFRACTION	16	chain 'E' and ((resid 115 through 127 ) or resid 1002)
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 128 through 148 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 149 through 163 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 164 through 174 )
20	X-RAY DIFFRACTION	20	chain 'F' and ((resid 7 through 57 ) or resid 1001)
21	X-RAY DIFFRACTION	21	chain 'F' and ((resid 58 through 104 ) or resid 1003)
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 105 through 114 )
23	X-RAY DIFFRACTION	23	chain 'F' and ((resid 115 through 127 ) or resid 1002)
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 128 through 150 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 151 through 163 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 164 through 176 )
27	X-RAY DIFFRACTION	27	chain 'G' and ((resid 7 through 57 ) or resid 1001)
28	X-RAY DIFFRACTION	28	chain 'G' and ((resid 58 through 104 ) or resid 1003)
29	X-RAY DIFFRACTION	29	chain 'G' and (resid 105 through 114 )
30	X-RAY DIFFRACTION	30	chain 'G' and ((resid 115 through 127 ) or resid 1002)
31	X-RAY DIFFRACTION	31	chain 'G' and (resid 128 through 140 )
32	X-RAY DIFFRACTION	32	chain 'G' and (resid 141 through 150 )
33	X-RAY DIFFRACTION	33	chain 'G' and (resid 151 through 163 )
34	X-RAY DIFFRACTION	34	chain 'G' and (resid 164 through 175 )
35	X-RAY DIFFRACTION	35	chain 'H' and ((resid 6 through 57 ) or resid 1001)
36	X-RAY DIFFRACTION	36	chain 'H' and ((resid 58 through 104 ) or resid 1003)
37	X-RAY DIFFRACTION	37	chain 'H' and (resid 105 through 114 )
38	X-RAY DIFFRACTION	38	chain 'H' and ((resid 115 through 127 ) or resid 1002)
39	X-RAY DIFFRACTION	39	chain 'H' and (resid 128 through 163 )
40	X-RAY DIFFRACTION	40	chain 'H' and (resid 164 through 174 )

-
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

-
Protein , 2 types, 8 molecules ABCDEFGH

-
Non-polymers , 6 types, 40 molecules

-
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

-Protein , 2 types, 8 molecules ABCDEFGH

-Non-polymers , 6 types, 40 molecules

-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

-
Protein , 2 types, 8 molecules ABCDEFGH

-
Non-polymers , 6 types, 40 molecules

-
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