PDB-6l9c: Neutron structure of copper amine oxidase from Arthrobacter glibi...

ID or keywords:

Entry

Database: PDB / ID: 6l9c

Title

Neutron structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4

Components

Phenylethylamine oxidase

Keywords

OXIDOREDUCTASE / Copper amine oxidase / topaquinone / TPQ

Function / homology

Function and homology information

primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / quinone binding / copper ion binding
Similarity search - Function

Biological species

Arthrobacter globiformis (bacteria)

Method

X-RAY DIFFRACTION / NEUTRON DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.14 Å

Authors

Murakawa, T. / Kurihara, K. / Shoji, M. / Shibazaki, C. / Sunami, T. / Tamada, T. / Yano, N. / Yamada, T. / Kusaka, K. / Suzuki, M. ...

Funding support

Japan, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharing.
Authors: Murakawa, T. / Kurihara, K. / Shoji, M. / Shibazaki, C. / Sunami, T. / Tamada, T. / Yano, N. / Yamada, T. / Kusaka, K. / Suzuki, M. / Shigeta, Y. / Kuroki, R. / Hayashi, H. / Yano, T. / ...

History

Deposition	Nov 8, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 29, 2020	Provider: repository / Type: Initial release
Revision 1.1	May 20, 2020	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	Jun 3, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Nov 22, 2023	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 / 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_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.ptnr2_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6l9c.cif.gz	341.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6l9c.ent.gz	281.6 KB	Display	PDB format
PDBx/mmJSON format	6l9c.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6l9c_validation.pdf.gz	395.6 KB	Display	wwPDB validaton report
Full document	6l9c_full_validation.pdf.gz	400.6 KB	Display
Data in XML	6l9c_validation.xml.gz	16.4 KB	Display
Data in CIF	6l9c_validation.cif.gz	33.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l9/6l9c ftp://data.pdbj.org/pub/pdb/validation_reports/l9/6l9c	HTTPS FTP

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Related structure data

Related structure data	3wa2S S: Starting model for refinement
Similar structure data	1sii-d 1sih-d 2cg1-d 2cfl-d 1avk-d 1rjo-d 2cg0-d 2bt3-d 1w5z-d 3kn4-d 1av4-d 2cfw-d 1avl-d 3wa2-d 2e2t-d 2cfk-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

X: Phenylethylamine oxidase

hetero molecules

69.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

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

Unit cell

Length a, b, c (Å)	157.548, 61.779, 92.332
Angle α, β, γ (deg.)	90.000, 112.130, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	X-1064- HOH
2	1	X-1352- HOH
3	1	X-1467- HOH
4	1	X-1735- HOH
5	1	X-1787- HOH

#1: Protein	Phenylethylamine oxidase / Primary amine oxidase Mass: 68993.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P46881, primary-amine oxidase
#2: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1063 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Sequence details	The protein contains microheterogeneity at position 382 (E9C versus TPQ).

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Experiment

Experiment

Method	Number of used crystals
X-RAY DIFFRACTION	1
NEUTRON DIFFRACTION	1

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Sample preparation

Crystal	Density Matthews: 3 Å³/Da / Density % sol: 58.95 %
Crystal grow	Temperature: 289 K / Method: microdialysis / pH: 7.4 / Details: 1.05M potassium-sodium tartrate, 25mM HEPES

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	100	1	N
2	100	1	N

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	Photon Factory	BL-5A		1	1
SPALLATION SOURCE	JPARC MLF	BL-03	J-PARC MLF BEAMLINE BL-03	2	3.0-5.7

Detector

Type	ID	Detector	Date	Details
ADSC QUANTUM 315r	1	CCD	May 31, 2016
DECTRIS PILATUS 6M	2	PIXEL	Nov 10, 2015	Ni-Ti supermirror neutron guide Detector: iBIXDetector type: WSF PSD (Wavelength Shift Fiber Position Sensitive Detector)

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	LAUE	L	neutron	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1	1
2	3	1
3	5.7	1

Reflection

B_iso Wilson estimate: 16.56 Å² / Entry-ID: 6L9C

Resolution (Å)	Num. obs	% possible obs (%)	Redundancy (%)	R_merge(I) obs	R_pim(I) all	R_rim(I) all	Χ²	Diffraction-ID	Net I/σ(I)
1.14-50	296297	99.4	5.2	0.069	0.029	0.076	3.114	1	14.8
1.72-20.94	203273	87.4	2.6639		0.1249			2	4.99

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.14-1.16	3.5	0.801	14901	0.703	0.504	0.95	1.53	99.9
1.16-1.18	3.5	0.71	14749	0.746	0.446	0.841	1.544	99.8
1.18-1.2	3.5	0.629	14848	0.775	0.394	0.746	1.558	99.8
1.2-1.23	3.5	0.553	14777	0.828	0.344	0.654	1.632	99.8
1.23-1.25	3.5	0.494	14815	0.862	0.307	0.584	1.664	99.8
1.25-1.28	3.6	0.433	14870	0.889	0.269	0.511	1.679	99.8
1.28-1.32	3.6	0.375	14776	0.912	0.233	0.443	1.831	99.8
1.32-1.35	3.6	0.314	14833	0.932	0.194	0.371	1.806	99.8
1.35-1.39	3.6	0.264	14807	0.951	0.163	0.311	1.912	99.8
1.39-1.44	3.6	0.223	14883	0.964	0.138	0.263	2.027	99.8
1.44-1.49	3.6	0.186	14848	0.973	0.115	0.22	2.283	99.9
1.49-1.55	3.5	0.149	14860	0.981	0.093	0.176	2.496	99.9
1.55-1.62	5.6	0.148	14873	0.988	0.067	0.163	2.847	100
1.62-1.7	7	0.128	14882	0.992	0.052	0.138	3.102	100
1.7-1.81	6.9	0.104	14938	0.994	0.043	0.113	3.43	100
1.81-1.95	6.6	0.085	14905	0.994	0.037	0.093	3.874	100
1.95-2.15	9.6	0.081	14938	0.996	0.028	0.086	3.99	100
2.15-2.46	9.5	0.071	14967	0.996	0.025	0.075	4.19	100
2.46-3.09	9.1	0.063	15022	0.996	0.024	0.067	4.413	99.8
3.09-50	6.3	0.056	13805	0.992	0.027	0.062	4.493	90.6

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
HKL-2000		data scaling
PDB_EXTRACT	3.25	data extraction
HKL-2000		data reduction
PHASER		phasing

Refinement

% reflection R_free: 5 % / Cross valid method: THROUGHOUT / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Method to determine structure	Starting model	Resolution (Å)	Refine-ID	B_iso max (Å²)	B_iso mean (Å²)	B_iso min (Å²)	R_factor R_free	R_factor R_work	R_factor obs	Num. reflection R_free	Num. reflection R_work	Num. reflection obs	% reflection obs (%)	SU ML	σ(F)	Phase error
MOLECULAR REPLACEMENT	3WA2 3wa2	1.14-45.03	X-RAY DIFFRACTION	125.14	27.8236	12.32	0.1815	0.1677	0.1684	14805	281300	296105	99.28	0.12	1.33	22.69
		1.72-20.951	NEUTRON DIFFRACTION				0.2095	0.18	0.1815	3813		76237	87.23		0

Refinement step

Cycle: final / Resolution: 1.14→45.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4890	0	2	2667	7559
B_iso mean	-	-	19.28	38.2	-
Num. residues	-	-	-	-	622

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	13146
X-RAY DIFFRACTION	f_angle_d	1.318	21509
X-RAY DIFFRACTION	f_chiral_restr	0.102	804
X-RAY DIFFRACTION	f_plane_restr	0.007	2364
X-RAY DIFFRACTION	f_dihedral_angle_d	22.036	3336

LS refinement shell

R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.72-1.7418	0.3428	97	0.3215	1824	NEUTRON DIFFRACTION	60
1.7418-1.7647	0.3047	107	0.3254	2046	NEUTRON DIFFRACTION	66
1.7647-1.7889	0.3555	115	0.3075	2195	NEUTRON DIFFRACTION	73
1.7889-1.8144	0.3613	121	0.3004	2304	NEUTRON DIFFRACTION	75
1.8144-1.8415	0.3203	125	0.287	2389	NEUTRON DIFFRACTION	78
1.8415-1.8702	0.297	127	0.2961	2407	NEUTRON DIFFRACTION	78
1.8702-1.9009	0.3444	128	0.2699	2423	NEUTRON DIFFRACTION	80
1.9009-1.9336	0.3738	133	0.2619	2510	NEUTRON DIFFRACTION	81
1.9336-1.9688	0.2774	136	0.2496	2605	NEUTRON DIFFRACTION	84
1.9688-2.0066	0.2668	137	0.2401	2602	NEUTRON DIFFRACTION	86
2.0066-2.0475	0.2487	143	0.2299	2728	NEUTRON DIFFRACTION	89
2.0475-2.092	0.2547	146	0.2204	2762	NEUTRON DIFFRACTION	90
2.092-2.1406	0.2624	148	0.2104	2827	NEUTRON DIFFRACTION	92
2.1406-2.1941	0.23	151	0.2023	2858	NEUTRON DIFFRACTION	94
2.1941-2.2534	0.2645	146	0.1866	2792	NEUTRON DIFFRACTION	91
2.2534-2.3196	0.2219	148	0.1738	2801	NEUTRON DIFFRACTION	92
2.3196-2.3944	0.2195	154	0.1631	2914	NEUTRON DIFFRACTION	95
2.3944-2.4798	0.1759	157	0.1574	2973	NEUTRON DIFFRACTION	96
2.4798-2.5789	0.1634	155	0.1553	2954	NEUTRON DIFFRACTION	96
2.5789-2.6961	0.1852	157	0.1555	2987	NEUTRON DIFFRACTION	97
2.6961-2.8379	0.1918	161	0.1582	3032	NEUTRON DIFFRACTION	98
2.8379-3.0152	0.1774	158	0.1563	3017	NEUTRON DIFFRACTION	98
3.0152-3.2472	0.1844	161	0.1521	3045	NEUTRON DIFFRACTION	98
3.2472-3.5726	0.134	156	0.1254	2960	NEUTRON DIFFRACTION	96
3.5726-4.0862	0.1341	156	0.1104	2968	NEUTRON DIFFRACTION	96
4.0862-5.1356	0.1241	152	0.1079	2880	NEUTRON DIFFRACTION	92
5.1356-20.951	0.1568	138	0.136	2621	NEUTRON DIFFRACTION	82
1.14-1.153	0.3207	484	0.3071	9197	X-RAY DIFFRACTION	98
1.153-1.1666	0.2962	495	0.3009	9402	X-RAY DIFFRACTION	100
1.1666-1.1808	0.3179	494	0.2919	9383	X-RAY DIFFRACTION	100
1.1808-1.1957	0.2996	493	0.2879	9369	X-RAY DIFFRACTION	100
1.1957-1.2115	0.2855	497	0.2766	9431	X-RAY DIFFRACTION	100
1.2115-1.2281	0.263	493	0.268	9368	X-RAY DIFFRACTION	100
1.2281-1.2456	0.2638	493	0.2655	9363	X-RAY DIFFRACTION	100
1.2456-1.2642	0.2678	498	0.2644	9455	X-RAY DIFFRACTION	100
1.2642-1.284	0.2485	494	0.25	9364	X-RAY DIFFRACTION	100
1.284-1.305	0.26	490	0.2454	9327	X-RAY DIFFRACTION	100
1.305-1.3275	0.2304	494	0.244	9389	X-RAY DIFFRACTION	100
1.3275-1.3517	0.2579	495	0.2336	9405	X-RAY DIFFRACTION	100
1.3517-1.3777	0.2713	495	0.2297	9418	X-RAY DIFFRACTION	100
1.3777-1.4058	0.2522	495	0.2261	9401	X-RAY DIFFRACTION	100
1.4058-1.4364	0.2452	495	0.2199	9393	X-RAY DIFFRACTION	100
1.4364-1.4698	0.2201	495	0.215	9410	X-RAY DIFFRACTION	100
1.4698-1.5065	0.2213	496	0.2105	9401	X-RAY DIFFRACTION	100
1.5065-1.5473	0.2196	492	0.1995	9382	X-RAY DIFFRACTION	100
1.5473-1.5928	0.2023	495	0.1925	9411	X-RAY DIFFRACTION	100
1.5928-1.6442	0.2046	497	0.1836	9436	X-RAY DIFFRACTION	100
1.6442-1.703	0.2002	495	0.1781	9408	X-RAY DIFFRACTION	100
1.703-1.7712	0.1864	499	0.1767	9483	X-RAY DIFFRACTION	100
1.7712-1.8518	0.1998	495	0.1739	9423	X-RAY DIFFRACTION	100
1.8518-1.9494	0.1739	498	0.1671	9460	X-RAY DIFFRACTION	100
1.9494-2.0715	0.1731	499	0.1585	9475	X-RAY DIFFRACTION	100
2.0715-2.2315	0.1676	499	0.1487	9467	X-RAY DIFFRACTION	100
2.2315-2.456	0.1682	499	0.1442	9485	X-RAY DIFFRACTION	100
2.456-2.8114	0.167	502	0.1503	9543	X-RAY DIFFRACTION	100
2.8114-3.5418	0.1478	492	0.1421	9340	X-RAY DIFFRACTION	98
3.5418-45.03	0.153	447	0.1412	8511	X-RAY DIFFRACTION	88

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