PDB-4z40: Active site complex BamBC of Benzoyl Coenzyme A reductase as isolated

ID or keywords:

Entry

Database: PDB / ID: 4z40

Title

Active site complex BamBC of Benzoyl Coenzyme A reductase as isolated

Components

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

Keywords

OXIDOREDUCTASE / aromatics / 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 /

SAD / Resolution: 2.35 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	Jun 24, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jul 1, 2015	Group: Database references
Revision 1.2	Jul 8, 2015	Group: Database references
Revision 1.3	Jul 29, 2015	Group: Database references
Revision 1.4	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	4z40.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb4z40.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	4z40.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4z40_validation.pdf.gz	3.7 MB	Display	wwPDB validaton report
Full document	4z40_full_validation.pdf.gz	3.8 MB	Display
Data in XML	4z40_validation.xml.gz	110.6 KB	Display
Data in CIF	4z40_validation.cif.gz	148.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z4/4z40 ftp://data.pdbj.org/pub/pdb/validation_reports/z4/4z40	HTTPS FTP

-
Related structure data

Related structure data	4z3wC 4z3xC 4z3yC 4z3zC 1aorS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4z3x-2 4z3x-1 4z3z-2 6tgh-d 4pkc-1 2d4v-d 6yrw-d 1b6s-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

386 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 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

hetero molecules

defined by author&software
193 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Benzoyl-CoA reductase, putative

C: Benzoyl-CoA reductase, putative

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

defined by author&software
193 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	125.190, 116.820, 143.600
Angle α, β, γ (deg.)	90.00, 110.39, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain 'A' and (resseq 1:652 )
2	1	1	chain 'B' and (resseq 1:652 )
3	1	1	chain 'C' and (resseq 1:652 )
4	1	1	chain 'D' and (resseq 1:652 )

-
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 , 7 types, 179 molecules

#3: Chemical	ChemComp-UNL / UNKNOWN LIGAND Num. of mol.: 4 / Source method: obtained synthetically
#4: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe₄S₄
#5: 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
#6: Chemical	ChemComp-W / TUNGSTEN ION Mass: 183.840 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: W
#7: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#8: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.62 Å³/Da / Density % sol: 53 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 8% PEG 4000, 0.2 M LiCl, 2 mM DTT, 0.1 M Tris pH 8.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.214 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.214 Å / Relative weight: 1
Reflection	Resolution: 2.35→49.502 Å / Num. all: 161382 / Num. obs: 159502 / % possible obs: 98.8 % / Redundancy: 4.66 % / R_sym value: 0.17 / Net I/σ(I): 5.6
Reflection shell	Resolution: 2.35→2.41 Å / Redundancy: 4.63 % / R_merge(I) obs: 0.253 / Mean I/σ(I) obs: 0.84 / % possible all: 99.1

-
Processing

Software

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

Refinement

Method to determine structure:

SAD
Starting model: 1AOR

1aor

Resolution: 2.35→49.502 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.27 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2379	1593	1 %
R_work	0.2123	-	-
obs	0.2125	158727	98.45 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.35→49.502 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25818	0	336	139	26293

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	26955
X-RAY DIFFRACTION	f_angle_d	0.958	36449
X-RAY DIFFRACTION	f_dihedral_angle_d	14.301	10163
X-RAY DIFFRACTION	f_chiral_restr	0.038	3891
X-RAY DIFFRACTION	f_plane_restr	0.004	4688

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	5180	X-RAY DIFFRACTION	POSITIONAL
1	2	B	5180	X-RAY DIFFRACTION	POSITIONAL	0.022
1	3	C	5180	X-RAY DIFFRACTION	POSITIONAL	0.022
1	4	D	5180	X-RAY DIFFRACTION	POSITIONAL	0.023

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 (%)
2.35-2.4259	0.4325	143	0.4162	14234	X-RAY DIFFRACTION	99
2.4259-2.5126	0.4	147	0.3803	14276	X-RAY DIFFRACTION	99
2.5126-2.6131	0.3795	140	0.3506	14209	X-RAY DIFFRACTION	98
2.6131-2.7321	0.3649	145	0.3271	14288	X-RAY DIFFRACTION	99
2.7321-2.8761	0.3011	149	0.295	14349	X-RAY DIFFRACTION	99
2.8761-3.0563	0.3172	145	0.2712	14316	X-RAY DIFFRACTION	99
3.0563-3.2922	0.3042	145	0.2605	14269	X-RAY DIFFRACTION	99
3.2922-3.6234	0.245	142	0.2295	14289	X-RAY DIFFRACTION	99
3.6234-4.1475	0.2339	146	0.1944	14229	X-RAY DIFFRACTION	98
4.1475-5.2245	0.1741	144	0.1633	14330	X-RAY DIFFRACTION	98
5.2245-49.5126	0.1764	147	0.1508	14345	X-RAY DIFFRACTION	97

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	0.5095	0.176	0.2446	0.243	0.1313	0.4659	1.1423	-0.0989	1.395	-0.3481	-0.2843	-0.4072	-1.2633	-0.3759	-0.1497	1.6583	0.3005	1.0722	0.6593	0.0949	1.8083	-8.5118	57.866	37.2375
2	0.0532	0.2271	-0.1578	0.6684	-0.4929	0.3774	0.6938	0.9865	1.1665	-1.162	-0.2831	0.0155	-0.8602	-0.378	-0.2946	2.1222	0.7216	0.6701	1.6085	0.5986	1.4861	-4.5414	52.4738	8.553
3	0.326	-0.1534	-0.2397	0.2668	-0.0742	0.3529	0.8181	1.3926	1.0919	-1.1971	-0.2909	-0.0152	-1.5588	-1.1808	-0.373	2.5217	1.2702	0.8365	1.6677	0.9517	1.8	-16.3103	61.9753	13.2567
4	0.4729	0.0039	0.2508	0.3142	-0.1844	0.1586	0.8055	0.4558	0.7662	-0.4334	-0.1803	0.6117	-0.8165	-1.1033	0.1888	1.5891	1.0817	0.6014	1.62	0.5194	1.6257	-30.5358	57.2852	27.3106
5	2.094	-0.4923	-0.5841	1.8468	0.8515	1.79	0.0474	0.1602	-0.0281	-0.4112	0.0526	-0.5958	-0.2497	0.0803	-0.0934	0.5135	0.0432	0.2488	0.5136	0.0306	0.9347	-29.3777	56.6145	69.4907
6	0.7248	-0.8263	-0.3944	4.338	0.5026	0.8687	0.0585	-0.5641	-0.115	1.154	-0.194	-1.0355	0.2163	0.1728	0.1545	0.8576	0.0596	-0.1403	1.0231	0.1095	1.1549	-28.8595	47.3341	100.7932
7	0.7152	-0.2381	-0.1056	1.7823	0.6732	1.165	-0.0381	-0.2161	-0.2171	0.0313	0.1377	-0.8941	0.1254	0.4068	-0.0705	0.4323	0.0358	0.0222	0.6856	0.0462	1.1378	-19.7395	54.1542	89.2895
8	2.2445	0.1303	-0.7123	1.8296	-0.2436	2.2963	-0.3497	0.6142	-0.7278	0.0211	-0.1089	0.3037	0.6285	-0.3811	0.3714	0.6334	-0.165	0.2605	0.8247	-0.3198	1.0586	-89.4662	23.5427	84.1844
9	2.4846	0.6639	-1.0816	0.7519	-1.3868	4.5349	0.0392	-0.2999	-0.0305	0.3612	-0.0732	0.1745	-0.4843	0.2843	0.0155	0.589	-0.0537	0.1157	0.6888	-0.1179	0.726	-79.4709	42.3295	101.916
10	2.73	-0.4551	-1.1116	1.8425	-0.4908	2.6626	-0.128	0.1307	-0.3025	0.4651	0.0471	0.5763	-0.0593	-0.3292	0.0766	0.5447	-0.0934	0.2085	0.7053	-0.1178	0.8594	-96.3114	38.6582	102.0636
11	1.2356	0.9726	0.6567	1.5709	0.0834	0.7671	-0.1479	0.3821	-0.5183	0.4348	-0.1313	0.8122	0.5431	-1.1087	0.2114	0.7121	-0.2502	0.3588	1.2882	-0.2931	1.4856	-112.5758	30.5849	98.2363
12	2.241	0.4351	-0.7043	1.6884	-0.1346	1.915	0.1266	-0.4799	-0.1461	-0.1521	-0.1042	-0.2529	-0.0058	0.4145	-0.0093	0.6192	-0.0121	0.2812	0.6178	0.0035	0.7788	47.4136	23.8065	15.5536
13	1.6509	-0.3924	-0.3582	1.2778	0.7634	4.1502	0.3269	0.2255	0.3815	-0.3676	-0.0696	-0.0145	-0.8977	-0.1595	-0.2937	0.91	0.0605	0.3892	0.5715	0.0404	1.0158	37.3927	42.0909	0.0956
14	2.2864	0.4887	-0.5482	0.8609	-0.2607	1.2962	0.2097	-0.3067	0.0821	-0.215	-0.0984	-0.3693	-0.1661	0.4816	-0.093	0.8312	-0.0384	0.3951	0.6603	-0.0281	0.9393	60.0238	34.6721	1.04
15	2.0341	-1.0453	-0.4015	1.8592	0.448	1.1524	0.3741	-0.6125	0.4812	0.143	-0.1738	-0.0925	-0.5713	0.3682	-0.232	0.8841	-0.2643	0.4257	1.0373	-0.2172	0.9394	37.0782	39.6449	35.6841
16	3.2695	0.6845	-1.0541	1.9628	-0.1493	1.3416	0.5131	-0.4618	0.303	0.0609	-0.1637	0.0907	-0.6202	0.2425	-0.3248	0.7164	-0.0802	0.3066	0.6383	-0.0791	0.7879	25.3261	31.0116	31.0524
17	1.8874	2.6464	-0.0362	6.2567	-1.7684	1.1685	0.7178	-0.3935	0.2066	0.6104	-0.5043	0.1727	-0.3577	0.0105	-0.2093	0.8223	-0.2537	0.2497	1.2422	-0.1107	0.903	34.4724	28.1693	42.2645
18	2.7024	-0.5485	-0.9828	1.1793	0.1207	1.559	0.4203	-0.8469	0.8652	0.2857	0.1401	-0.1528	-0.8513	1.0298	-0.5219	1.2229	-0.4535	0.4627	1.0336	-0.3835	1.175	36.9379	46.5936	37.402
19	2.2842	-1.4753	-1.7866	3.3504	-2.6875	7.7572	0.5549	-0.1508	-0.1087	0.5179	0.2151	0.4564	-1.2885	0.1702	-0.69	1.2281	-0.1313	0.1152	1.5613	-0.0363	1.1496	5.7843	36.4513	57.0487
20	1.4952	0.1192	-1.8633	0.6851	-0.3501	2.3806	0.1999	0.0295	-0.0299	0.13	0.1104	-0.1113	0.055	-0.1892	-0.2136	1.2987	0.1123	0.2131	1.4396	0.007	1.1299	5.6832	22.3355	61.1812
21	3.3401	0.3346	-1.0722	0.7921	-0.3685	1.8291	0.7216	-0.2809	0.7051	-0.303	-0.0376	-0.4635	-0.6582	0.3628	-0.5722	0.6668	0.0023	0.3003	0.5044	-0.0463	0.7392	8.9483	35.3843	35.2749
22	2.301	-0.8354	-0.0074	3.8199	2.1649	5.5086	0.2454	-0.6631	0.3366	0.1121	-0.1214	-0.3746	0.1529	0.9951	-0.1032	0.9303	-0.0874	0.12	1.5414	-0.0861	1.1017	12.7829	26.2156	54.4924
23	2.6105	0.7299	-0.5015	2.3941	-0.2394	2.0754	-0.228	0.3456	-0.4886	-0.3773	-0.0329	-0.3336	0.2693	-0.1143	0.2653	0.455	0.0039	0.1645	0.4737	-0.0373	0.9015	-43.2476	32.4552	68.6788
24	3.865	0.0379	-0.8454	1.8663	-0.2952	2.7264	0.0035	0.5701	-0.2849	-0.2919	-0.1249	-0.2056	0.1835	-0.2632	0.1253	0.4864	0.0014	0.1567	0.5948	-0.061	0.6912	-51.3311	37.5904	67.3219
25	8.1813	-0.6272	-0.4771	5.2344	1.0178	4.0913	0.7418	-0.1501	-0.2014	-0.3436	-0.1182	0.3472	-0.4226	-0.0259	-0.5918	0.8557	-0.0578	0.1465	1.323	-0.3232	0.996	-61.1214	20.5674	59.1283
26	0.7063	1.4019	0.3009	8.7709	-4.1104	6.4038	-0.118	0.2081	-0.4211	-0.075	-0.1749	0.5101	0.0703	-0.0737	0.2575	0.7689	-0.0764	0.1687	1.4635	-0.2231	0.9336	-52.4713	34.8293	46.9958
27	2.0135	-0.4813	-2.9377	2.5423	1.4594	4.5195	0.2559	0.8525	-0.0549	-0.5399	-0.2441	0.1914	-0.3433	-0.4873	-0.0317	2.3271	-0.8214	0.2539	1.7004	-0.2744	0.8177	-48.1602	37.1448	36.0928
28	3.6509	-0.3276	-0.6289	2.6048	-0.0052	1.6802	-0.1366	0.5011	-0.4615	-0.303	-0.0317	-0.1531	0.1632	-0.4898	0.1584	0.4574	-0.1086	0.1139	0.8013	-0.1464	0.616	-70.0683	37.6512	70.6187
29	3.3282	-1.0098	-0.7999	2.0753	0.4946	2.7171	0.1087	0.9379	0.0192	-0.4083	-0.1722	-0.0032	-0.111	-0.6377	0.0239	0.5559	-0.0495	0.1365	0.9472	-0.1507	0.6953	-73.2541	42.2327	64.0792
30	4.2528	0.4163	0.7008	3.1471	0.1521	4.3062	-0.2382	1.173	-0.7413	-1.3582	-0.0069	-0.8124	0.6567	0.6545	0.1771	1.3147	-0.0809	0.4759	1.1845	-0.2477	0.9477	-44.0574	33.1027	44.2972

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 233 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 234 through 317 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 318 through 531 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 532 through 652 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 233 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 234 through 278 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 279 through 652 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 1 through 233 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 234 through 354 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 355 through 564 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 565 through 652 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 1 through 257 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 258 through 349 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 350 through 652 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 6 through 43 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 44 through 104 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 105 through 114 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 115 through 140 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 141 through 163 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 164 through 174 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 7 through 140 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 141 through 176 )
23	X-RAY DIFFRACTION	23	chain 'G' and (resid 7 through 43 )
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 44 through 140 )
25	X-RAY DIFFRACTION	25	chain 'G' and (resid 141 through 150 )
26	X-RAY DIFFRACTION	26	chain 'G' and (resid 151 through 163 )
27	X-RAY DIFFRACTION	27	chain 'G' and (resid 164 through 175 )
28	X-RAY DIFFRACTION	28	chain 'H' and (resid 6 through 94 )
29	X-RAY DIFFRACTION	29	chain 'H' and (resid 95 through 150 )
30	X-RAY DIFFRACTION	30	chain 'H' and (resid 151 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://pdbjlvh1.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 , 7 types, 179 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 , 7 types, 179 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 , 7 types, 179 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