PDB-6y9d: Crystal structure of the quaternary ammonium Rieske monooxygenase...

ID or keywords:

Entry

Database: PDB / ID: 6y9d

Title

Crystal structure of the quaternary ammonium Rieske monooxygenase CntA in complex with substrate L-Carnitine

Components

Carnitine monooxygenase oxygenase subunit

Keywords

OXIDOREDUCTASE / Apo / Rieske / Iron-Sulphur Cluster

Function / homology

Function and homology information

carnitine monooxygenase / carnitine metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / dioxygenase activity / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.97 Å

Authors

Quareshy, M. / Shanmugam, M. / Bugg, T.D. / Cameron, A. / Chen, Y.

Funding support

United Kingdom, 1items

Citation

Journal: J.Biol.Chem. / Year: 2020
Title: Structural basis of carnitine monooxygenase CntA substrate specificity, inhibition, and intersubunit electron transfer.
Authors: Quareshy, M. / Shanmugam, M. / Townsend, E. / Jameson, E. / Bugg, T.D.H. / Cameron, A.D. / Chen, Y.

History

Deposition	Mar 6, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 18, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jul 21, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	6y9d.cif.gz	1.7 MB	Display	PDBx/mmCIF format
PDB format	pdb6y9d.ent.gz	1.4 MB	Display	PDB format
PDBx/mmJSON format	6y9d.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6y9d_validation.pdf.gz	14.5 MB	Display	wwPDB validaton report
Full document	6y9d_full_validation.pdf.gz	14.6 MB	Display
Data in XML	6y9d_validation.xml.gz	163.8 KB	Display
Data in CIF	6y9d_validation.cif.gz	218.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y9/6y9d ftp://data.pdbj.org/pub/pdb/validation_reports/y9/6y9d	HTTPS FTP

-
Related structure data

Related structure data	6y8jC 6y8sC 6zgpC 3vcpS 6y9c C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6zgp-3 6zgp-4 6zgp-2 6zgp-1 6y9c-1 6y8j-1 6y8s-1 6kji-d 2igt-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) 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

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#137 - May 2011 Cytochrome bc1 similarity (5) #36 - Dec 2002 Cytochrome c similarity (5) #117 - Sep 2009 Xanthine Oxidoreductase similarity (1) #144 - Dec 2011 Complex I similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #111 - Mar 2009 Hydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #82 - Oct 2006 Cytochrome p450 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#137 - May 2011
Cytochrome bc1
similarity (5)
#36 - Dec 2002
Cytochrome c
similarity (5)
#117 - Sep 2009
Xanthine Oxidoreductase
similarity (1)
#144 - Dec 2011
Complex I
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#111 - Mar 2009
Hydrogenase
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#82 - Oct 2006
Cytochrome p450
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Carnitine monooxygenase oxygenase subunit

B: Carnitine monooxygenase oxygenase subunit

C: Carnitine monooxygenase oxygenase subunit

D: Carnitine monooxygenase oxygenase subunit

E: Carnitine monooxygenase oxygenase subunit

F: Carnitine monooxygenase oxygenase subunit

G: Carnitine monooxygenase oxygenase subunit

H: Carnitine monooxygenase oxygenase subunit

I: Carnitine monooxygenase oxygenase subunit

J: Carnitine monooxygenase oxygenase subunit

K: Carnitine monooxygenase oxygenase subunit

L: Carnitine monooxygenase oxygenase subunit

hetero molecules

546 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Carnitine monooxygenase oxygenase subunit

B: Carnitine monooxygenase oxygenase subunit

C: Carnitine monooxygenase oxygenase subunit

hetero molecules

defined by author&software
Evidence: gel filtration
136 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Carnitine monooxygenase oxygenase subunit

E: Carnitine monooxygenase oxygenase subunit

F: Carnitine monooxygenase oxygenase subunit

hetero molecules

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

3

G: Carnitine monooxygenase oxygenase subunit

H: Carnitine monooxygenase oxygenase subunit

I: Carnitine monooxygenase oxygenase subunit

hetero molecules

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

4

J: Carnitine monooxygenase oxygenase subunit

K: Carnitine monooxygenase oxygenase subunit

L: Carnitine monooxygenase oxygenase subunit

hetero molecules

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

Unit cell

Length a, b, c (Å)	91.590, 177.770, 158.800
Angle α, β, γ (deg.)	90.000, 90.170, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain B
3	1	chain C
4	1	chain D
5	1	chain E
6	1	chain F
7	1	chain G
8	1	chain H
9	1	chain I
10	1	chain J
11	1	chain K
12	1	chain L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 4 - 371 / Label seq-ID: 24 - 391

Dom-ID	Selection details	Auth asym-ID	Label asym-ID
1	chain A	A	A
2	chain B	B	B
3	chain C	C	C
4	chain D	D	D
5	chain E	E	E
6	chain F	F	F
7	chain G	G	G
8	chain H	H	H
9	chain I	I	I
10	chain J	J	J
11	chain K	K	K
12	chain L	L	L

-
Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein	Carnitine monooxygenase oxygenase subunit / Carnitine monooxygenase alpha subunit Mass: 44780.172 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: antA_2, antA_1, antA_3, A7M79_02670, A7M90_13970, ABUW_3074, B4R90_07590, B9X95_06095, BGC29_09330, C2U32_18540, C3415_14505, CBI29_00874, CHQ89_11265, CPI82_11190, CSB70_0522, DLI75_01970, ...Gene: antA_2, antA_1, antA_3, A7M79_02670, A7M90_13970, ABUW_3074, B4R90_07590, B9X95_06095, BGC29_09330, C2U32_18540, C3415_14505, CBI29_00874, CHQ89_11265, CPI82_11190, CSB70_0522, DLI75_01970, DOL94_04925, DVA79_16365, E2533_13315, E2536_16135, E5294_15630, E5979_13670, EA685_07170, EA686_01565, EA706_03020, EA722_03860, EA746_003300, EWO92_12480, EWO96_16565, EWP49_15025, FD887_09300, FD913_14110, FJU36_15000, FJU42_16200, FJU76_14830, FJU79_08840, FJU87_10695, FJV14_20515, LV38_02893, NCTC13305_01609, SAMEA104305283_02985, SAMEA104305351_01970 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A059ZPP5, carnitine monooxygenase

#1: Protein

Carnitine monooxygenase oxygenase subunit / Carnitine monooxygenase alpha subunit

Mass: 44780.172 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Acinetobacter baumannii (bacteria)
Gene: antA_2, antA_1, antA_3, A7M79_02670, A7M90_13970, ABUW_3074, B4R90_07590, B9X95_06095, BGC29_09330, C2U32_18540, C3415_14505, CBI29_00874, CHQ89_11265, CPI82_11190, CSB70_0522, DLI75_01970, ...
Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A059ZPP5, carnitine monooxygenase

-
Non-polymers , 6 types, 1062 molecules

#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER Mass: 175.820 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe₂S₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-152 / CARNITINE / (3-CARBOXY-2-(R)-HYDROXY-PROPYL)-TRIMETHYL-AMMONIUM Mass: 162.207 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₇H₁₆NO₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-SCN / THIOCYANATE ION Mass: 58.082 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CNS
#6: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1002 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 48.87 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 10mM HEPES, 20% PEG3350 (w/v), 0.2M NaSCN, 0.5mM TCEP PH range: 7.0 - 7.6

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.3 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 10, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.3 Å / Relative weight: 1
Reflection	Resolution: 1.97→81.42 Å / Num. obs: 353116 / % possible obs: 98.82 % / Redundancy: 3.3 % / B_iso Wilson estimate: 30.38 Å² / CC_1/2: 0.984 / CC star: 0.996 / R_merge(I) obs: 0.1489 / R_pim(I) all: 0.09601 / R_rim(I) all: 0.1778 / Net I/σ(I): 5.18
Reflection shell	Resolution: 1.97→2.04 Å / Redundancy: 3 % / R_merge(I) obs: 0.9578 / Mean I/σ(I) obs: 1.21 / Num. unique obs: 35196 / CC_1/2: 0.638 / CC star: 0.883 / R_pim(I) all: 0.6599 / R_rim(I) all: 1.168 / % possible all: 98.47

-
Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
PDB_EXTRACT	3.25	data extraction
DIALS		data reduction
DIALS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3VCP

3vcp

Resolution: 1.97→81.419 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.49 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2471	31463	4.99 %
R_work	0.2097	599397	-
obs	0.2116	353116	89.06 %

Solvent computation

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

Displacement parameters

B_iso max: 176.2 Å² / B_iso mean: 45.6863 Å² / B_iso min: 16.04 Å²

Refinement step

Cycle: final / Resolution: 1.97→81.419 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	34344	0	612	1002	35958
B_iso mean	-	-	72.35	39.14	-
Num. residues	-	-	-	-	4224

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	12972	X-RAY DIFFRACTION	4.89	TORSIONAL
1	2	B	12972	X-RAY DIFFRACTION	4.89	TORSIONAL
1	3	C	12972	X-RAY DIFFRACTION	4.89	TORSIONAL
1	4	D	12972	X-RAY DIFFRACTION	4.89	TORSIONAL
1	5	E	12972	X-RAY DIFFRACTION	4.89	TORSIONAL
1	6	F	12972	X-RAY DIFFRACTION	4.89	TORSIONAL
1	7	G	12972	X-RAY DIFFRACTION	4.89	TORSIONAL
1	8	H	12972	X-RAY DIFFRACTION	4.89	TORSIONAL
1	9	I	12972	X-RAY DIFFRACTION	4.89	TORSIONAL
1	10	J	12972	X-RAY DIFFRACTION	4.89	TORSIONAL
1	11	K	12972	X-RAY DIFFRACTION	4.89	TORSIONAL
1	12	L	12972	X-RAY DIFFRACTION	4.89	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.97-1.9924	0.376	1007	0.3669	18329	81
1.9924-2.0158	0.3828	1063	0.3462	18576	83
2.0158-2.0404	0.3812	1019	0.3357	19064	85
2.0404-2.0662	0.3546	1013	0.3172	19216	86
2.0662-2.0934	0.3462	1092	0.3076	19446	87
2.0934-2.1221	0.3354	1006	0.3015	19611	87
2.1221-2.1524	0.3091	1004	0.2862	19490	87
2.1524-2.1846	0.3146	1034	0.2837	19839	88
2.1846-2.2187	0.3218	995	0.276	19573	88
2.2187-2.2551	0.3083	1014	0.2761	19448	87
2.2551-2.294	0.3035	1016	0.2677	19883	88
2.294-2.3357	0.2882	1018	0.2568	19914	89
2.3357-2.3806	0.294	1124	0.2532	19989	89
2.3806-2.4292	0.2696	1035	0.2391	19977	89
2.4292-2.482	0.2759	1025	0.2363	20140	89
2.482-2.5398	0.2897	1161	0.2401	19905	90
2.5398-2.6033	0.2791	1098	0.2346	20148	90
2.6033-2.6737	0.2786	1035	0.2293	19967	89
2.6737-2.7524	0.2703	1087	0.226	20135	90
2.7524-2.8412	0.2717	1000	0.2247	20411	90
2.8412-2.9428	0.2579	995	0.2131	20555	91
2.9428-3.0606	0.2442	1090	0.2055	20467	91
3.0606-3.1999	0.2454	941	0.2104	20552	91
3.1999-3.3686	0.2538	1141	0.2086	20608	92
3.3686-3.5796	0.2318	1056	0.1908	20619	92
3.5796-3.856	0.205	1040	0.1753	20912	93
3.856-4.2441	0.1796	1019	0.1556	21021	93
4.2441-4.8581	0.1812	1108	0.1438	21013	94
4.8581-6.1204	0.1872	1194	0.1553	21039	94
6.1204-81.4	0.2207	1033	0.1888	19550	87

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	1.2373	0.1227	-0.291	0.5374	0.2413	2.2018	0.0366	0.0457	-0.0461	-0.0275	0.052	-0.1846	-0.0807	0.7079	-0.0798	0.2533	0.005	-0.0892	0.4068	-0.0485	0.3414	39.2064	-7.2493	63.7204
2	4.2021	-1.855	1.8316	5.7435	-0.45	7.2508	0.3648	-1.2466	-1.2838	0.6676	-0.2201	-0.0523	1.2727	0.0047	-0.2867	0.52	0.0569	-0.0639	0.6038	0.1597	0.5281	22.7211	-17.4114	89.0556
3	2.8528	-0.2889	0.0984	1.558	0.7729	2.0986	-0.0423	-0.3016	-0.3625	0.2286	0.0787	-0.0781	0.2035	0.4095	0.0216	0.2476	0.0312	-0.0914	0.2375	0.0401	0.3149	26.9812	-13.5212	78.4149
4	0.9322	-0.4754	0.0634	0.3857	0.4614	2.9315	0.0241	0.2814	0.1572	-0.0994	-0.126	0.0694	-0.1782	-0.8297	0.0625	0.2352	0.0416	-0.0638	0.4821	0.0259	0.3198	-6.6512	-7.3816	59.2973
5	1.8609	0.2099	-0.6902	0.6467	0.1972	2.4996	-0.043	0.0567	-0.0188	0.0863	-0.0801	0.1581	0.1527	-0.7979	0.1032	0.191	-0.0287	-0.0169	0.3217	-0.0162	0.3145	-5.0741	-12.7619	71.1422
6	6.7584	-0.8957	-2.8725	1.3419	-0.8988	2.5882	-0.5756	0.7261	-1.6624	-0.6042	-0.1469	0.8409	0.6814	-1.0227	0.4605	0.5592	-0.2901	-0.0523	1.3455	-0.2538	0.8161	-17.699	-21.0234	38.6721
7	1.2195	0.006	-0.7772	0.9588	0.419	3.1586	-0	0.3773	-0.1389	-0.0235	-0.1594	0.2188	0.496	-1.3623	0.0473	0.3172	-0.1633	-0.0688	0.8193	-0.0738	0.4005	-11.2015	-16.8317	48.0608
8	3.0351	0.9605	0.4307	1.2555	0.6118	3.6639	0.0637	-0.0365	0.1808	-0.1287	-0.0073	-0.001	-0.2539	-0.0806	-0.0353	0.2844	0.0428	-0.0142	0.1608	0.0187	0.2334	20.855	-5.2985	28.6996
9	2.8654	0.2275	0.0035	0.7149	0.4457	2.8643	0.0443	0.2719	-0.0201	-0.1627	-0.0295	0.124	0.0509	-0.5035	-0.049	0.297	0.0034	-0.0748	0.2984	0.0044	0.2415	10.4512	-11.6157	23.6492
10	3.7472	1.749	-0.7152	4.0105	-3.3419	6.2212	0.0656	0.1135	-0.8351	-1.0681	-0.1454	-0.8357	1.4216	1.2929	0.128	0.6721	0.1346	-0.0011	0.8715	-0.213	0.6609	45.4197	-15.6033	27.5569
11	1.8679	0.2656	0.7779	1.1267	0.3135	3.6398	0.1403	0.1858	-0.2457	-0.0401	0.1264	-0.2435	0.2427	0.7147	-0.2225	0.2773	0.0549	-0.0398	0.3756	-0.0384	0.2939	33.9377	-12.9218	29.2005
12	2.8899	-0.6573	-1.6859	0.9465	0.7346	2.2898	0.0678	-0.112	0.2859	0.0169	0.0417	-0.1186	-0.267	0.381	-0.1199	0.2711	-0.0481	-0.0831	0.2405	-0.0148	0.291	79.7684	-5.9633	-11.7278
13	2.1506	-0.0333	-1.1244	0.209	0.1544	2.0434	-0.0336	-0.1574	-0.0046	0.0382	0.0127	-0.1055	-0.0361	0.5651	0.0341	0.2352	-0.0086	-0.0805	0.4073	-0.0117	0.3136	89.4874	-11.5568	-18.5461
14	6.1385	1.598	2.4987	4.616	0.3208	7.177	0.5034	-1.4089	-1.3477	0.5951	-0.1835	-0.3355	1.0071	-0.3084	-0.355	0.4757	0.0632	-0.0488	0.6144	0.1207	0.5968	68.3552	-17.95	9.4794
15	3.081	-0.577	-0.6945	1.2712	0.5626	2.1861	-0.1459	-0.4152	-0.1965	0.1637	0.0645	0.0085	0.1852	0.491	0.0597	0.2532	0.0108	-0.0568	0.2897	0.021	0.2697	72.8879	-14.4025	-1.0633
16	1.8825	0.1002	0.0685	0.5444	-0.0514	2.448	0.0166	0.0959	0.0771	-0.0594	-0.0007	0.1013	-0.137	-0.2653	-0.0128	0.212	0.0156	-0.0499	0.2142	0.0291	0.2381	60.801	-8.8668	-53.6882
17	4.1156	1.8269	0.8005	7.5278	-6.366	9.1995	0.3341	0.5426	-1.0742	-1.0256	-0.2814	-0.7027	1.4014	1.6465	-0.0856	0.4903	0.1079	-0.0625	0.84	-0.1645	0.5736	90.8922	-18.485	-51.4929
18	1.4664	0.4826	0.8614	1.1676	0.2786	2.7487	0.0803	0.0403	-0.1875	0.0522	0.0342	-0.2144	0.1415	0.4931	-0.1081	0.1918	0.0135	-0.0473	0.3108	0.0134	0.2806	79.6126	-14.6278	-50.1054
19	1.345	-0.2267	0.0616	0.5843	-0.4258	2.1204	-0.0017	0.3294	0.3262	-0.0424	-0.0007	0.0321	-0.3413	-0.4314	0.048	0.2724	0.0987	-0.0525	0.3527	0.0487	0.3302	39.7253	-0.4839	-28.5586
20	4.8086	0.7752	0.4993	1.0103	0.0162	3.1403	0.0053	-0.2825	0.1231	0.1375	-0.0774	-0.0267	-0.0328	-0.3344	0.08	0.2313	0.0416	-0.0275	0.1521	-0.0146	0.233	46.7099	-11.8874	0.6747
21	2.2343	-0.0913	-0.565	0.8179	0.0797	1.8978	-0.0159	0.263	0.0557	0.0752	0.0515	0.1231	0.0529	-0.54	-0.0333	0.197	0.0096	-0.0427	0.3968	0.0423	0.2942	31.8026	-11.2605	-19.5847
22	4.4406	-2.9796	-1.8206	3.608	-0.2859	2.1374	-0.13	0.6526	-1.0243	-0.202	-0.304	1.154	0.6221	-0.9671	0.3598	0.442	-0.1242	-0.0371	1.0269	-0.0064	0.6211	27.1457	-17.7219	-40.5311
23	1.5492	-0.1389	-0.86	0.9209	-0.2327	2.3131	0.0066	0.3957	-0.0403	-0.0684	-0.0097	0.1104	0.2168	-0.6348	-0.0002	0.2275	-0.0492	-0.0644	0.4841	0.0012	0.3116	34.0248	-14.1434	-31.3242
24	2.6145	-0.6794	-0.5954	0.9467	0.4465	2.4747	0.0248	-0.1012	-0.3252	0.0032	-0.0788	0.0089	0.3396	0.0117	0.0602	0.2766	-0.0067	-0.0381	0.1405	0.0524	0.2792	34.8498	-62.8065	-5.6912
25	2.1032	0.1895	-0.1772	0.6527	-0.0862	2.4976	0.0241	-0.1247	-0.0671	0.0779	-0.0301	0.1155	0.064	-0.4242	-0.0106	0.2275	0.0199	-0.0251	0.2046	0.0246	0.2322	23.9881	-57.4291	-0.8422
26	4.4808	-3.5049	1.505	4.6867	-4.0349	6.2854	-0.0051	-0.2003	0.7772	0.5779	-0.1661	-0.7713	-0.9945	1.5733	0.104	0.4573	-0.1028	-0.0586	0.6675	-0.1044	0.4998	58.5419	-50.0031	-5.1149
27	0.8633	-0.1468	-0.3657	1.1909	0.5344	2.3431	0.0005	-0.1443	0.0218	-0.044	0.039	-0.1167	0.02	0.5469	-0.0312	0.1843	0.0092	-0.0469	0.2813	0.0146	0.2551	47.3005	-53.9208	-6.5561
28	1.048	0.1595	-0.014	1.161	-1.1218	3.4017	0.0132	-0.0507	-0.1445	-0.0225	-0.0333	0.0156	0.1215	-0.291	0.0182	0.2236	-0.0543	-0.0591	0.2844	-0.0382	0.3187	7.669	-62.8258	-36.4151
29	1.7646	-0.0568	-0.4987	0.3654	-0.1349	1.621	-0.0443	0.1921	-0.0385	-0.064	-0.0333	0.0515	0.0344	-0.2528	0.0841	0.2687	-0.0313	-0.0822	0.2985	-0.0273	0.3435	8.7015	-57.2483	-48.2144
30	3.8663	3.0396	1.5614	2.8313	-0.2149	4.9535	-0.4186	-0.396	1.0379	0.1803	0.1278	1.2128	-1.1085	-0.7714	0.1788	0.541	0.1451	-0.0844	0.9148	-0.0181	0.6952	-5.1584	-50.7182	-16.17
31	1.8997	0.0755	1.1113	1.1655	-0.6321	2.9	-0.0434	-0.2571	0.0532	0.1064	0.0212	0.1338	-0.3001	-0.5306	0.0069	0.2317	0.0283	-0.0306	0.406	-0.0657	0.313	1.7907	-54.4348	-25.0919
32	3.1535	0.7719	1.0052	0.623	-0.1735	2.2087	0.1304	0.099	-0.2656	-0.0473	-0.1245	-0.0413	0.3832	0.0904	-0.0516	0.291	0.0543	-0.0057	0.2086	-0.059	0.3103	40.3676	-67.5715	-49.146
33	1.6359	0.2027	0.0275	0.7774	-0.0718	3.7374	-0.0428	-0.2552	0.0306	0.0982	-0.0052	-0.1815	0.0256	0.6436	0.0968	0.1961	0.0359	-0.0263	0.4137	-0.0117	0.3182	62.0071	-56.2124	-28.2066
34	3.3184	0.1269	0.1864	1.2669	0.3179	2.0857	-0.1737	0.4572	0.1255	-0.0096	0.0572	-0.1789	-0.014	0.5516	0.0752	0.2159	-0.0438	-0.0469	0.3673	0.0354	0.2583	52.1832	-56.7414	-51.3126
35	8.695	-2.6029	-4.0961	2.7315	3.5667	5.5855	0.1884	1.2011	1.4973	-0.6858	-0.083	-0.3077	-1.1222	0.1588	-0.0058	0.5371	-0.1087	-0.1114	0.6634	0.1946	0.6519	36.3871	-50.1258	-65.5897
36	3.0291	0.509	0.5475	1.4581	0.3955	1.6792	-0.1995	0.4795	0.3697	-0.1909	0.0624	0.037	-0.1741	0.3497	0.0981	0.226	-0.026	-0.048	0.3001	0.0663	0.286	40.9087	-53.8752	-55.2874
37	1.9733	0.0801	0.9477	1.0639	0.6343	3.2185	0.0415	-0.1194	-0.1027	0.1256	-0.1853	0.1077	0.2029	-0.7323	0.0982	0.2078	-0.0599	-0.0333	0.4611	-0.0245	0.3647	-38.8614	-60.8095	42.9547
38	2.5552	0.2635	0.3897	0.8054	0.5537	2.0371	-0.0379	0.1772	0.1391	-0.0988	-0.1538	0.1525	-0.1308	-0.5932	0.1626	0.2447	0.0357	-0.1093	0.4361	0.0303	0.3776	-37.2171	-55.419	31.0735
39	4.8292	1.8647	2.0296	6.2361	-1.4441	3.6571	-0.4325	-0.4909	1.0528	0.5953	-0.4078	1.0943	-1.4595	-1.1018	0.7429	0.822	0.23	-0.029	1.4318	-0.1463	0.6522	-50.1745	-47.4312	63.451
40	1.7499	0.2602	1.893	1.1428	0.6801	3.2765	-0.1255	-0.5299	0.2542	0.0992	-0.2792	0.3703	-0.3595	-1.2888	0.2125	0.3109	0.0992	-0.0342	0.7975	-0.1497	0.449	-43.654	-51.5403	54.1268
41	3.3655	0.0339	0.4316	1.2488	0.2151	3.3422	0.0642	-0.1234	-0.1421	-0.0042	0.0062	-0.2126	0.1851	0.3772	-0.1111	0.2324	0.0547	0.0127	0.2387	-0.032	0.2592	1.0398	-64.0358	34.4114
42	1.2117	-0.224	-0.2333	0.32	0.4553	2.4623	-0.0008	-0.28	0.199	0.0935	0.1222	-0.2695	0.0988	0.8617	-0.0418	0.2516	0.0033	-0.023	0.6057	-0.0702	0.4029	11.1291	-59.2582	41.4024
43	4.1795	-0.7487	-2.5751	2.6732	1.1277	7.4247	0.3106	1.2996	1.3876	-0.4848	-0.3115	-0.3571	-1.2284	-0.2773	-0.0397	0.5337	-0.0382	-0.0217	0.7401	0.2353	0.6616	-9.159	-50.4261	13.4914
44	3.0283	0.2816	-0.4276	1.5397	0.2235	2.1193	-0.0512	0.5146	0.3917	-0.1945	0.0766	-0.026	-0.1532	0.2262	-0.0091	0.2234	-0.0252	-0.005	0.3148	0.0671	0.3029	-5.0653	-54.7476	23.9872
45	2.4409	-0.3515	0.4169	1.0003	-0.1187	2.9134	0.1377	0.091	-0.2429	0.0512	-0.0445	0.0079	0.5696	-0.0343	-0.0768	0.4086	-0.0104	-0.0731	0.1063	0.0043	0.2471	-11.633	-62.911	73.5942
46	2.6731	-0.0774	0.3712	0.6649	0.3728	3.2958	0.1249	-0.2474	-0.0691	0.1915	-0.0911	0.1226	0.1646	-0.6562	-0.0558	0.362	-0.0356	-0.0088	0.2496	0.0143	0.2471	-22.0014	-56.5826	78.5354
47	4.3839	-1.0442	1.7119	6.4202	-3.8912	6.7128	-0.0375	-0.0228	0.6774	0.9138	0.0613	-0.8062	-0.9129	1.6923	-0.0561	0.4967	-0.0862	-0.0829	0.9294	-0.2376	0.567	12.9707	-52.2886	74.2376
48	1.3812	-0.0738	-0.7919	1.5481	0.5926	3.5661	0.0681	-0.1767	0.0796	0.1344	0.0934	-0.1731	0.1141	0.7989	-0.1463	0.3085	0.0061	-0.0845	0.3513	-0.0438	0.2911	1.4692	-55.2702	72.8779

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 203 )	A	4 - 203
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 204 through 229 )	A	204 - 229
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 230 through 371 )	A	230 - 371
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 4 through 83 )	B	4 - 83
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 84 through 203 )	B	84 - 203
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 204 through 229 )	B	204 - 229
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 230 through 371 )	B	230 - 371
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 4 through 83 )	C	4 - 83
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 84 through 203 )	C	84 - 203
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 204 through 229 )	C	204 - 229
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 230 through 371 )	C	230 - 371
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 4 through 83 )	D	4 - 83
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 84 through 203 )	D	84 - 203
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 204 through 229 )	D	204 - 229
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 230 through 371 )	D	230 - 371
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 4 through 203 )	E	4 - 203
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 204 through 229 )	E	204 - 229
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 230 through 371 )	E	230 - 371
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 4 through 53 )	F	4 - 53
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 54 through 141 )	F	54 - 141
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 142 through 203 )	F	142 - 203
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 204 through 229 )	F	204 - 229
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 230 through 371 )	F	230 - 371
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 4 through 83 )	G	4 - 83
25	X-RAY DIFFRACTION	25	chain 'G' and (resid 84 through 203 )	G	84 - 203
26	X-RAY DIFFRACTION	26	chain 'G' and (resid 204 through 229 )	G	204 - 229
27	X-RAY DIFFRACTION	27	chain 'G' and (resid 230 through 371 )	G	230 - 371
28	X-RAY DIFFRACTION	28	chain 'H' and (resid 4 through 83 )	H	4 - 83
29	X-RAY DIFFRACTION	29	chain 'H' and (resid 84 through 203 )	H	84 - 203
30	X-RAY DIFFRACTION	30	chain 'H' and (resid 204 through 229 )	H	204 - 229
31	X-RAY DIFFRACTION	31	chain 'H' and (resid 230 through 371 )	H	230 - 371
32	X-RAY DIFFRACTION	32	chain 'I' and (resid 4 through 53 )	I	4 - 53
33	X-RAY DIFFRACTION	33	chain 'I' and (resid 54 through 141 )	I	54 - 141
34	X-RAY DIFFRACTION	34	chain 'I' and (resid 142 through 203 )	I	142 - 203
35	X-RAY DIFFRACTION	35	chain 'I' and (resid 204 through 229 )	I	204 - 229
36	X-RAY DIFFRACTION	36	chain 'I' and (resid 230 through 371 )	I	230 - 371
37	X-RAY DIFFRACTION	37	chain 'J' and (resid 4 through 83 )	J	4 - 83
38	X-RAY DIFFRACTION	38	chain 'J' and (resid 84 through 203 )	J	84 - 203
39	X-RAY DIFFRACTION	39	chain 'J' and (resid 204 through 229 )	J	204 - 229
40	X-RAY DIFFRACTION	40	chain 'J' and (resid 230 through 371 )	J	230 - 371
41	X-RAY DIFFRACTION	41	chain 'K' and (resid 4 through 83 )	K	4 - 83
42	X-RAY DIFFRACTION	42	chain 'K' and (resid 84 through 203 )	K	84 - 203
43	X-RAY DIFFRACTION	43	chain 'K' and (resid 204 through 229 )	K	204 - 229
44	X-RAY DIFFRACTION	44	chain 'K' and (resid 230 through 371 )	K	230 - 371
45	X-RAY DIFFRACTION	45	chain 'L' and (resid 4 through 83 )	L	4 - 83
46	X-RAY DIFFRACTION	46	chain 'L' and (resid 84 through 203 )	L	84 - 203
47	X-RAY DIFFRACTION	47	chain 'L' and (resid 204 through 229 )	L	204 - 229
48	X-RAY DIFFRACTION	48	chain 'L' and (resid 230 through 371 )	L	230 - 371

-
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 , 1 types, 12 molecules ABCDEFGHIJKL

-
Non-polymers , 6 types, 1062 molecules

-
Details

-
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 , 1 types, 12 molecules ABCDEFGHIJKL

-Non-polymers , 6 types, 1062 molecules

-Details

-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 , 1 types, 12 molecules ABCDEFGHIJKL

-
Non-polymers , 6 types, 1062 molecules

-
Details

-
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