PDB-4z3w: Active site complex BamBC of Benzoyl Coenzyme A reductase in comp...

ID or keywords:

Entry

Database: PDB / ID: 4z3w

Title

Active site complex BamBC of Benzoyl Coenzyme A reductase in complex with 1,5 Dienoyl-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: 2.208 Å

Authors

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

Funding support

Germany,

Switzerland, 4items

Organization	Grant number	Country
German Research Foundation	BO 1565/10-2	Germany
German Research Foundation	ER 222/5-2	Germany
Swiss National Science Foundation	P1SKP3-198452	Switzerland
Swiss National Science Foundation	P1SKP3-155073	Switzerland

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: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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	4z3w.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb4z3w.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	4z3w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z3/4z3w ftp://data.pdbj.org/pub/pdb/validation_reports/z3/4z3w	HTTPS FTP

-
Related structure data

Related structure data	4z3xC 4z3yC 4z3zC 4z40SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4z3y-d 4z3x-d 4z40-d 4z3z-d 7m7w-d 5dgy-1 4r83-d 1de4-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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)	125.340, 116.300, 144.160
Angle α, β, γ (deg.)	90.00, 110.48, 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 , 7 types, 547 molecules

#3: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER / 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-4KX / 1,5 Dienoyl-CoA / Cyclohex-1,5-diene-1-carbonyl-CoA Mass: 873.656 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₈H₄₂N₇O₁₇P₃S
#9: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 507 / 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: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 4.2 % PEG 4000, 0.2 M LiCl, 2 mM DTT, 1 mM ZnSO4 and 0.2 M Tris pH 8.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 27, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.999 Å / Relative weight: 1
Reflection	Resolution: 2.208→82.68 Å / Num. all: 194610 / Num. obs: 180047 / % possible obs: 92.5 % / Redundancy: 3.86 % / R_merge(I) obs: 0.115 / Net I/σ(I): 7.59
Reflection shell	Resolution: 2.208→2.34 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.67 / Mean I/σ(I) obs: 1.23 / % possible all: 63.6

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4Z40

4z40

Resolution: 2.208→82.63 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.66 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2222	2340	1.3 %
R_work	0.178	-	-
obs	0.1786	179952	92.57 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.208→82.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25815	0	556	507	26878

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	27203
X-RAY DIFFRACTION	f_angle_d	1.09	36845
X-RAY DIFFRACTION	f_dihedral_angle_d	16.196	10369
X-RAY DIFFRACTION	f_chiral_restr	0.044	3920
X-RAY DIFFRACTION	f_plane_restr	0.005	4786

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	5165	X-RAY DIFFRACTION	POSITIONAL
1	2	B	5165	X-RAY DIFFRACTION	POSITIONAL	0.03

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 (%)
2.2076-2.2526	0.3846	79	0.3401	5943	X-RAY DIFFRACTION	53
2.2526-2.3016	0.3509	99	0.2944	7503	X-RAY DIFFRACTION	67
2.3016-2.3551	0.3491	119	0.2746	8434	X-RAY DIFFRACTION	75
2.3551-2.414	0.3035	117	0.2589	9681	X-RAY DIFFRACTION	85
2.414-2.4793	0.3076	146	0.2504	10801	X-RAY DIFFRACTION	96
2.4793-2.5523	0.2754	140	0.2327	11156	X-RAY DIFFRACTION	99
2.5523-2.6347	0.2935	152	0.2225	11254	X-RAY DIFFRACTION	100
2.6347-2.7288	0.2632	147	0.2181	11233	X-RAY DIFFRACTION	100
2.7288-2.8381	0.2775	151	0.2193	11231	X-RAY DIFFRACTION	100
2.8381-2.9673	0.2633	144	0.2194	11255	X-RAY DIFFRACTION	100
2.9673-3.1237	0.2479	144	0.2147	11264	X-RAY DIFFRACTION	100
3.1237-3.3194	0.2682	155	0.2077	11261	X-RAY DIFFRACTION	100
3.3194-3.5757	0.2315	147	0.1889	11291	X-RAY DIFFRACTION	100
3.5757-3.9356	0.2046	149	0.1572	11261	X-RAY DIFFRACTION	100
3.9356-4.505	0.1686	152	0.133	11280	X-RAY DIFFRACTION	100
4.505-5.6757	0.1646	146	0.1202	11323	X-RAY DIFFRACTION	100
5.6757-82.6879	0.1592	153	0.1289	11441	X-RAY DIFFRACTION	99

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	1.5848	0.3815	-0.3151	1.2932	-0.2482	1.0322	-0.029	-0.1939	-0.2376	-0.1228	-0.0754	-0.1753	0.0951	0.1042	0.0695	0.3698	0.0205	0.1352	0.2191	0.0398	0.4001	47.4112	20.3321	16.0417
2	0.9359	0.3289	-0.5481	1.2202	-0.1514	1.2017	0.2997	0.1647	0.3663	-0.3875	-0.0247	-0.0727	-0.4749	-0.1804	-0.241	0.6735	0.0898	0.2258	0.3338	0.0693	0.5352	39.0357	42.6457	1.6237
3	0.3894	0.1425	-0.3349	0.9881	0.1261	0.394	-0.0335	0.3159	-0.0256	-1.0359	0.0668	-0.4799	-0.0998	-0.0259	0.1078	0.9205	0.021	0.2303	0.3132	0.0048	0.3287	46.2186	28.5225	-12.2254
4	1.1146	0.38	-0.7687	0.9497	-0.4536	1.276	0.1156	-0.2316	0.0153	-0.2617	-0.1271	-0.5906	-0.1679	0.2907	0.0534	0.5298	-0.0364	0.2545	0.3659	-0.0039	0.6857	66.5031	36.5611	7.2128
5	0.8359	0.1438	0.1392	0.5481	-0.1799	0.5151	0.5323	-0.006	1.0059	-0.3226	-0.0471	-0.2369	-0.6338	-0.2884	0.2157	0.8133	0.1584	0.5027	0.4008	0.0496	1.0366	-8.4194	56.4677	37.7369
6	0.2561	0.2997	-0.1541	0.3324	-0.1775	0.0816	0.4289	0.6209	0.6565	-0.6649	-0.1551	0.0521	-0.233	-0.2019	-0.1659	1.3128	0.4286	0.3568	1.0262	0.3808	0.8576	-6.745	51.6476	6.0259
7	0.0264	0.0138	0.0515	0.0083	-0.0039	0.0114	0.4336	0.4363	0.9729	-0.5084	-0.0531	-0.0972	-0.6025	-0.0697	0.98	1.4502	0.3588	0.6751	0.7551	0.546	1.5397	-5.2177	68.8321	14.9503
8	1.6591	-0.0163	0.2191	1.1605	-0.4651	0.2184	0.2306	0.4182	0.6253	-0.4283	0.1203	0.4005	-0.3013	-0.5468	-0.0102	0.853	0.333	0.1507	0.8959	0.3145	0.9307	-29.3461	52.2572	21.4666
9	1.5896	-0.1185	-0.2365	1.4297	0.3311	1.2377	0.0167	0.0741	-0.1754	-0.1924	-0.0002	-0.3475	-0.0756	0.0606	-0.0331	0.2617	0.0804	0.0717	0.3241	0.0431	0.476	-29.4479	54.5151	70.7882
10	0.9321	0.8522	0.0797	1.6545	0.9843	1.4127	0.035	-0.3015	-0.2004	0.4	-0.0978	-0.0987	0.2994	-0.0267	0.1002	0.3947	0.0694	-0.0701	0.4896	0.0881	0.4054	-37.0157	50.7568	96.1048
11	1.1355	-0.5175	-0.4202	0.916	0.3961	0.6628	0.0113	-0.3644	0.0068	0.1828	0.112	-0.5791	-0.0582	0.2862	-0.0188	0.2606	0.0483	-0.1273	0.4694	0.0154	0.5357	-23.971	61.0161	95.7263
12	1.2023	-0.2236	-0.2109	1.1205	0.2359	1.3394	-0.0607	-0.3052	-0.2127	0.1138	0.1678	-0.6625	0.0806	0.4679	-0.0279	0.3266	0.0993	-0.0473	0.6004	0.0413	0.9667	-8.7945	47.3877	83.5174
13	0.8825	-0.0143	-0.2576	0.6197	-0.0356	0.9337	-0.3182	0.3582	-0.986	0.1527	-0.1231	0.3783	0.6184	-0.1132	-0.3744	0.4439	-0.0854	0.1502	0.4523	-0.289	0.8906	-89.6237	20.2587	85.0193
14	1.7945	-0.135	-0.5281	1.7577	-0.7097	2.1158	0.0897	0.2054	0.1777	0.2266	-0.0534	0.2084	-0.5398	-0.0526	0.0177	0.3509	-0.0013	0.0336	0.3998	-0.078	0.3917	-88.5206	49.2243	89.5362
15	2.4534	0.3056	-1.7898	1.4856	-0.2419	2.9707	-0.0095	-0.3795	-0.2855	0.4106	-0.0772	0.1023	-0.1111	0.4347	0.1158	0.3936	-0.0102	0.0497	0.4057	-0.0275	0.393	-77.5591	39.3239	102.7859
16	1.5562	-0.2468	-0.6063	1.5096	-0.4349	1.3966	-0.2758	-0.3041	-0.5921	0.4716	0.0012	0.3293	0.2191	0.2125	0.2372	0.5668	0.0078	0.2328	0.43	0.0065	0.6188	-91.5299	32.4359	109.6317
17	0.8702	0.16	-0.4969	1.2871	-0.4027	1.0346	-0.1095	0.3786	-0.4231	0.358	-0.1157	1.0188	0.0518	-0.6041	-0.2015	0.3076	-0.067	0.1638	0.5551	-0.1869	0.8922	-108.7329	37.9666	94.3623
18	2.2921	-0.7579	0.1668	0.9237	-0.3112	1.1411	0.2043	-0.2691	0.3356	0.2146	-0.1384	0.1302	-0.2521	0.1671	-0.0713	0.4238	-0.0741	0.1505	0.3452	-0.0225	0.381	36.1691	36.0448	32.6832
19	1.6219	0.0852	-0.804	1.7012	-0.3573	0.8184	0.2513	-0.1115	0.1247	0.1033	-0.1068	0.0258	-0.2354	0.1233	-0.1255	0.3554	-0.0052	0.1355	0.2447	-0.0108	0.3653	22.9853	29.7124	32.3051
20	2.3875	1.4646	-0.5471	3.1239	-1.8205	2.0104	0.0142	-0.6719	-0.2018	0.5815	-0.3958	-0.2849	-0.115	-0.1817	-0.0477	0.4821	-0.0367	0.1069	0.4445	0.0295	0.365	34.4488	27.2032	42.0962
21	2.1633	-0.5139	-1.4182	1.464	0.0714	1.6185	0.2624	-0.3711	0.4448	-0.1574	-0.2422	0.0811	-0.5555	0.5733	-0.219	0.5438	-0.1672	0.1593	0.3501	-0.1108	0.3991	40.9589	43.0506	38.5439
22	0.7011	0.0278	0.1291	0.9349	-0.4306	0.2153	0.1786	-0.7248	0.3875	0.0929	0.0996	0.167	0.0044	0.4717	0.0628	0.5088	-0.1363	0.2454	0.437	-0.1522	0.657	28.8112	48.2755	39.4976
23	3.3236	0.5915	0.3205	4.8056	0.3996	3.4705	0.17	-0.5583	0.3283	0.0213	0.1763	0.2433	-0.3127	-0.2838	-0.4515	0.4774	-0.0272	0.0938	0.7096	-0.0091	0.6115	2.9311	32.1473	56.8694
24	2.5452	-0.0198	-2.3625	3.3321	0.4236	2.5617	0.3639	-0.7464	-0.3181	0.3171	0.3449	-0.2156	0.6158	0.3265	-0.4777	0.6481	-0.0365	-0.0097	0.855	0.1482	0.5768	6.4857	21.4069	61.8618
25	2.0693	0.4985	-1.0149	0.5811	-0.1941	1.0051	0.307	0.0183	0.4144	-0.1757	0.0162	-0.0773	-0.2888	-0.0892	-0.248	0.3648	0.0408	0.126	0.2289	-0.0102	0.3119	9.1507	36.0365	34.8415
26	2.5928	0.0431	-0.8753	0.542	0.4987	2.5522	0.4921	-0.1855	0.5983	-0.0429	0.003	-0.249	-0.3232	0.0655	-0.4388	0.3586	-0.0324	0.1099	0.3303	-0.0714	0.39	13.0745	37.5405	41.894
27	2.1001	-0.076	-0.257	0.4715	-0.0004	1.9064	0.1616	0.0342	0.1044	-0.2623	-0.0218	-0.0705	0.1116	-0.3075	-0.1005	0.4285	0.0111	0.0214	0.2578	0.0188	0.2645	3.4233	24.5785	29.6693
28	3.7916	-0.9457	-0.2355	4.6289	2.0081	2.7818	0.3373	-0.0207	-0.4709	-0.0776	-0.5591	-0.3961	0.0419	0.4811	-0.0557	0.6487	0.1119	0.0314	0.6412	0.1152	0.5732	19.2323	15.8083	41.4672
29	2.9272	1.0297	0.4782	4.7261	1.564	4.0562	0.0893	-0.2238	0.1274	-0.0538	-0.1138	-0.6134	0.3795	0.6004	0.0251	0.3546	-0.0807	0.0308	0.827	-0.0366	0.441	12.4487	29.0594	55.648
30	4.592	-1.119	2.0263	5.0442	-0.9847	0.9448	0.1567	-0.8269	-0.2621	0.7521	0.2133	0.166	-0.4159	-0.3912	-0.2195	0.5324	-0.0683	-0.0327	1.1093	-0.1074	0.3185	7.347	29.8744	67.1665
31	1.5893	-0.2818	-0.3063	1.138	0.0896	0.8525	-0.0405	0.2677	-0.467	-0.2706	-0.0364	-0.4466	0.1458	-0.1066	0.1242	0.2665	0.0162	0.0467	0.3604	-0.0686	0.4296	-49.4052	36.7748	68.8791
32	1.6021	0.1653	-0.2116	1.3433	0.0667	2.587	0.1497	0.3611	0.3578	-0.4379	-0.1778	0.02	-0.2173	0.07	-0.0073	0.3548	0.0318	0.0791	0.5373	-0.0353	0.4244	-54.9838	41.7868	64.0182
33	1.3459	-0.2219	-0.3553	1.6353	-0.0531	1.919	-0.1785	0.4354	-0.6249	-0.2632	-0.069	-0.3758	0.2602	0.0141	0.2066	0.3275	-0.0013	0.1296	0.365	-0.1038	0.6359	-45.782	27.031	68.1086
34	4.0885	0.1039	-0.768	2.3883	0.3457	2.0918	0.4138	-0.0701	-0.1378	-0.3455	-0.0447	0.2899	-0.2876	-0.0374	-0.3883	0.584	-0.0904	0.091	0.7434	-0.1416	0.714	-61.2872	19.5433	59.25
35	3.3959	0.8667	0.1068	4.1843	-0.2207	4.5359	-0.3758	0.7327	-0.3629	-0.7057	-0.2459	0.3725	-0.033	-0.2158	0.2959	0.5272	-0.0898	0.0299	1.1126	-0.2786	0.4981	-52.5155	33.7385	47.2555
36	1.0944	-0.4244	-0.5292	0.2885	0.0675	1.222	0.2575	0.3539	0.0727	-0.43	-0.1487	-0.1026	-0.5061	-0.0794	-0.0975	1.4754	-0.4079	0.1326	1.4393	-0.0933	0.393	-47.1623	36.2984	36.6673
37	2.3617	-0.6765	-0.5544	2.5567	-0.6864	5.2189	0.1942	0.8709	0.5765	-0.6205	-0.2806	-0.0699	-0.3174	0.17	0.0851	0.5273	0.0477	-0.013	0.6455	0.0651	0.411	-65.4575	51.3955	61.9717
38	1.0565	0.6211	1.1344	1.5813	-0.0164	1.6384	0.135	0.4868	-0.6186	-0.2428	-0.128	0.1801	-0.0117	-0.2506	-0.0963	0.2321	0.0094	-0.0045	0.6256	-0.22	0.3707	-78.5637	37.1001	71.9315
39	2.5849	-0.8405	0.7503	1.134	0.5379	1.7483	-0.1027	0.5093	-0.5797	-0.1263	-0.1478	-0.0575	0.2399	-0.1074	0.2445	0.2807	-0.0679	0.0821	0.4916	-0.1054	0.4855	-62.2797	32.935	71.2498
40	2.1364	0.3778	0.6614	2.8233	1.4317	1.5188	0.1651	0.3956	-0.8717	-0.1073	-0.1269	-0.2769	0.468	-0.5554	0.1231	0.3139	-0.0756	0.0812	0.5852	-0.1813	0.5683	-66.1655	30.1601	68.767
41	1.4704	0.9029	0.6369	4.5372	1.9916	1.5944	-0.1074	0.6939	-0.3166	-0.4621	-0.1559	0.145	0.24	-0.0593	0.07	0.4722	-0.0567	0.0063	0.8585	-0.2596	0.4024	-75.2461	32.1067	59.6646
42	2.0038	-0.2907	-0.6031	1.74	0.0661	0.6102	0.3187	0.7541	0.2808	-0.2569	-0.2218	0.1987	-0.0469	-0.3115	0.0782	0.3664	0.0842	-0.0389	0.7233	-0.0469	0.3964	-80.1757	47.8292	65.4577
43	2.0819	-0.6382	-1.3513	1.8651	0.68	1.1104	0.0201	0.392	0.6462	-0.3974	0.1319	-0.1626	-0.158	-0.2962	-0.1664	0.2774	0.0119	-0.0018	0.5255	-0.0091	0.4615	-68.0554	51.8978	66.5351
44	2.8977	-0.2798	-0.166	2.7158	1.0728	2.9753	-0.3211	0.7462	-0.7237	-0.548	0.0237	-0.5527	0.5014	0.3898	0.1641	0.6708	-0.086	0.162	0.943	-0.4095	0.7905	-42.5312	35.261	46.9084
45	0.0542	-0.0632	0.0971	0.0939	-0.0481	0.3735	0.011	-0.0922	0.0562	-0.218	0.0932	-0.2594	0.268	-0.2127	0.1222	1.1132	-0.5661	0.4398	1.3642	-0.673	1.0411	-47.1314	26.3634	40.647

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 349 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 350 through 451 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 452 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 297 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 298 through 433 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 434 through 652 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 1 through 243 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 244 through 349 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 350 through 481 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 482 through 653 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 1 through 213 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 214 through 263 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 264 through 349 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 350 through 481 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 482 through 652 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 7 through 57 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 58 through 104 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 105 through 114 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 115 through 127 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 128 through 149 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 150 through 163 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 164 through 174 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 7 through 84 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 85 through 114 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 115 through 140 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 141 through 150 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 151 through 163 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 164 through 176 )
31	X-RAY DIFFRACTION	31	chain 'G' and (resid 7 through 84 )
32	X-RAY DIFFRACTION	32	chain 'G' and (resid 85 through 104 )
33	X-RAY DIFFRACTION	33	chain 'G' and (resid 105 through 140 )
34	X-RAY DIFFRACTION	34	chain 'G' and (resid 141 through 150 )
35	X-RAY DIFFRACTION	35	chain 'G' and (resid 151 through 163 )
36	X-RAY DIFFRACTION	36	chain 'G' and (resid 164 through 175 )
37	X-RAY DIFFRACTION	37	chain 'H' and (resid 6 through 15 )
38	X-RAY DIFFRACTION	38	chain 'H' and (resid 16 through 57 )
39	X-RAY DIFFRACTION	39	chain 'H' and (resid 58 through 84 )
40	X-RAY DIFFRACTION	40	chain 'H' and (resid 85 through 104 )
41	X-RAY DIFFRACTION	41	chain 'H' and (resid 105 through 114 )
42	X-RAY DIFFRACTION	42	chain 'H' and (resid 115 through 127 )
43	X-RAY DIFFRACTION	43	chain 'H' and (resid 128 through 150 )
44	X-RAY DIFFRACTION	44	chain 'H' and (resid 151 through 163 )
45	X-RAY DIFFRACTION	45	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 , 7 types, 547 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, 547 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, 547 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