PDB-8j6g: Neutron structure of copper amine oxidase from Arthrobacter globi...

ID or keywords:

Entry

Database: PDB / ID: 8j6g

Title

Neutron structure of copper amine oxidase from Arthrobacter globiformis anaerobically reduced by phenylethylamine at pD 9.0

Components

Phenylethylamine oxidase

Keywords

OXIDOREDUCTASE / topaquinone

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: 1.09 Å

Authors

Murakawa, T. / Okajima, T.

Funding support

Japan, 1items

Citation

Journal: Acs Catalysis / Year: 2023
Title: Neutron Crystallography of a Semiquinone Radical Intermediate of Copper Amine Oxidase Reveals a Substrate-Assisted Conformational Change of the Peptidyl Quinone Cofactor
Authors: Murakawa, T. / Kurihara, K. / Shoji, M. / Yano, N. / Kusaka, K. / Kawano, Y. / Suzuki, M. / Shigeta, Y. / Yano, T. / Adachi, M. / Tanizawa, K. / Okajima, T.

History

Deposition	Apr 25, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 20, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8j6g.cif.gz	351.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8j6g.ent.gz	288.3 KB	Display	PDB format
PDBx/mmJSON format	8j6g.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8j6g_validation.pdf.gz	447.7 KB	Display	wwPDB validaton report
Full document	8j6g_full_validation.pdf.gz	449.1 KB	Display
Data in XML	8j6g_validation.xml.gz	15.9 KB	Display
Data in CIF	8j6g_validation.cif.gz	32.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j6/8j6g ftp://data.pdbj.org/pub/pdb/validation_reports/j6/8j6g	HTTPS FTP

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Related structure data

Related structure data	3wa2S S: Starting model for refinement
Similar structure data	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

A: Phenylethylamine oxidase

hetero molecules

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

1

A: Phenylethylamine oxidase

hetero molecules

A: Phenylethylamine oxidase

hetero molecules

defined by author&software
Evidence: gel filtration
138 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	157.220, 62.144, 92.344
Angle α, β, γ (deg.)	90.00, 112.22, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-966- HOH
2	1	A-1052- HOH
3	1	A-1252- HOH
4	1	A-1668- HOH
5	1	A-1716- HOH

#1: Protein	Phenylethylamine oxidase / Primary amine oxidase Mass: 69014.852 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: Chemical	ChemComp-PEA / 2-PHENYLETHYLAMINE Mass: 122.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₂N / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1009 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.03 Å³/Da / Density % sol: 59.35 %
Crystal grow	Temperature: 289 K / Method: microdialysis Details: 1.05 M potassium-sodium tartrate in 25 mM HEPES buffer, pH 7.4.

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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	2.716-5.335

Detector

Type	ID	Detector	Date
DECTRIS PILATUS 6M	1	PIXEL	May 22, 2018
iBIX	2	DIFFRACTOMETER	Apr 5, 2018

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	2.716	1
3	5.335	1

Reflection

Entry-ID: 8J6G

Resolution (Å)	Num. obs	% possible obs (%)	Redundancy (%)	CC_1/2	R_merge(I) obs	R_rim(I) all	Diffraction-ID	Net I/σ(I)	R_pim(I) all
1.09-50	650618	97.4	3.238	0.995	0.052	0.062	1	9.58
1.67-21.37	92713	96.9	5.5811				2	4.85	0.1235

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.09-1.16	0.264	102659	0.948	0.321	1
1.16-1.24	0.172	97906	0.971	0.208	1
1.24-1.34	0.123	92298	0.984	0.147	1
1.34-1.47	0.084	84940	0.989	0.102	1
1.47-1.64	0.062	77292	0.993	0.073	1
1.64-1.89	0.05	68064	0.993	0.06	1
1.89-2.32	0.045	57785	0.994	0.054	1
2.32-3.27	0.047	44918	0.993	0.056	1
3.27-50	0.048	24756	0.992	0.057	1

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Processing

Software

Name	Version	Classification
PHENIX	(1.19.2_4158: ???)	refinement
XDS		data scaling
XDS		data reduction
PHASER		phasing

Refinement

SU ML: 0.21 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 19.85 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 3WA2

3wa2

/ Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)	Refine-ID	R_factor R_free	R_factor R_work	R_factor obs	Num. reflection R_free	Num. reflection obs	% reflection R_free (%)	% reflection obs (%)	Diffraction-ID
1.09-44.55	X-RAY DIFFRACTION	0.1608	0.1513	0.1518	4636	337074	5	96.8	1
1.67-21.37	NEUTRON DIFFRACTION	0.2252	0.1981	0.1995		92709	5	96.8	2

Refinement step

Cycle: LAST / Resolution: 1.09→44.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4876	0	11	1009	5896

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	13837
X-RAY DIFFRACTION	f_angle_d	1.381	22544
X-RAY DIFFRACTION	f_dihedral_angle_d	17.786	3441
X-RAY DIFFRACTION	f_chiral_restr	0.102	835
X-RAY DIFFRACTION	f_plane_restr	0.011	2386

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 (%)
1.09-1.11	0.2691	541	0.2704	10259	X-RAY DIFFRACTION	96
1.11-1.12	0.2378	557	0.2506	10587	X-RAY DIFFRACTION	99
1.12-1.13	0.236	559	0.2362	10615	X-RAY DIFFRACTION	100
1.13-1.15	0.2464	559	0.2249	10629	X-RAY DIFFRACTION	100
1.15-1.16	0.204	558	0.2151	10586	X-RAY DIFFRACTION	99
1.16-1.18	0.211	558	0.2068	10594	X-RAY DIFFRACTION	100
1.18-1.2	0.225	564	0.2025	10744	X-RAY DIFFRACTION	100
1.2-1.21	0.2049	558	0.1963	10604	X-RAY DIFFRACTION	100
1.21-1.23	0.1928	560	0.1933	10638	X-RAY DIFFRACTION	100
1.23-1.25	0.2038	560	0.1912	10637	X-RAY DIFFRACTION	100
1.25-1.27	0.2081	560	0.1917	10637	X-RAY DIFFRACTION	100
1.27-1.3	0.197	564	0.1891	10725	X-RAY DIFFRACTION	100
1.3-1.32	0.196	561	0.1837	10666	X-RAY DIFFRACTION	100
1.32-1.35	0.1771	560	0.1764	10636	X-RAY DIFFRACTION	100
1.35-1.38	0.1964	561	0.1744	10669	X-RAY DIFFRACTION	100
1.38-1.41	0.18	563	0.1671	10695	X-RAY DIFFRACTION	100
1.41-1.45	0.1829	561	0.1672	10653	X-RAY DIFFRACTION	100
1.45-1.49	0.1727	565	0.1591	10749	X-RAY DIFFRACTION	100
1.49-1.53	0.1659	560	0.1552	10623	X-RAY DIFFRACTION	100
1.53-1.58	0.1578	561	0.1559	10661	X-RAY DIFFRACTION	100
1.58-1.63	0.1663	565	0.1517	10735	X-RAY DIFFRACTION	100
1.63-1.7	0.1522	561	0.148	10664	X-RAY DIFFRACTION	100
1.67-1.69	0.341	133	0.3237	2531	X-RAY DIFFRACTION	84
1.69-1.71	0.3312	139	0.3184	2645	X-RAY DIFFRACTION	88
1.7-1.78	0.1571	565	0.1522	10740	X-RAY DIFFRACTION	100
1.71-1.73	0.3146	143	0.3102	2700	X-RAY DIFFRACTION	90
1.73-1.75	0.3367	142	0.3066	2704	X-RAY DIFFRACTION	90
1.75-1.77	0.3117	148	0.3121	2802	X-RAY DIFFRACTION	92
1.77-1.8	0.3437	146	0.2997	2778	X-RAY DIFFRACTION	92
1.78-1.87	0.1531	564	0.1521	10702	X-RAY DIFFRACTION	100
1.8-1.82	0.3402	149	0.2863	2841	X-RAY DIFFRACTION	94
1.82-1.85	0.2875	149	0.2754	2832	X-RAY DIFFRACTION	95
1.85-1.88	0.2954	157	0.2694	2963	X-RAY DIFFRACTION	97
1.87-1.99	0.1476	565	0.147	10717	X-RAY DIFFRACTION	100
1.88-1.91	0.2878	154	0.2589	2925	X-RAY DIFFRACTION	98
1.91-1.94	0.2893	155	0.2514	2959	X-RAY DIFFRACTION	98
1.94-1.98	0.2353	155	0.2375	2954	X-RAY DIFFRACTION	99
1.98-2.02	0.256	161	0.232	3033	X-RAY DIFFRACTION	99
1.99-2.14	0.155	564	0.1407	10734	X-RAY DIFFRACTION	100
2.02-2.06	0.2459	157	0.2214	2994	X-RAY DIFFRACTION	99
2.06-2.1	0.2314	157	0.2221	2995	X-RAY DIFFRACTION	99
2.1-2.15	0.2332	157	0.2027	3001	X-RAY DIFFRACTION	99
2.14-2.36	0.1434	563	0.132	10717	X-RAY DIFFRACTION	100
2.15-2.21	0.2393	159	0.1929	2996	X-RAY DIFFRACTION	100
2.21-2.27	0.2138	160	0.1813	3046	X-RAY DIFFRACTION	100
2.27-2.33	0.1766	157	0.1709	2983	X-RAY DIFFRACTION	100
2.33-2.41	0.2136	161	0.1672	3060	X-RAY DIFFRACTION	100
2.36-2.7	0.1548	568	0.1381	10784	X-RAY DIFFRACTION	100
2.41-2.49	0.1989	160	0.1519	3032	X-RAY DIFFRACTION	100
2.49-2.59	0.1893	158	0.1537	3030	X-RAY DIFFRACTION	100
2.59-2.71	0.1915	161	0.1497	3045	X-RAY DIFFRACTION	100
2.7-3.4	0.1517	570	0.1402	10823	X-RAY DIFFRACTION	100
2.71-2.85	0.1605	160	0.1523	3036	X-RAY DIFFRACTION	100
2.85-3.03	0.2099	159	0.152	3021	X-RAY DIFFRACTION	100
3.03-3.27	0.1836	161	0.144	3062	X-RAY DIFFRACTION	100
3.27-3.59	0.1587	160	0.1217	3043	X-RAY DIFFRACTION	100
3.4-44.55	0.1286	580	0.1191	10996	X-RAY DIFFRACTION	100
3.59-4.11	0.1335	161	0.1115	3024	X-RAY DIFFRACTION	100
4.11-5.16	0.1325	161	0.1161	3059	X-RAY DIFFRACTION	99
5.17-21.37	0.1592	156	0.1422	2979	X-RAY DIFFRACTION	94

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