PDB-5zp4: Copper amine oxidase from Arthrobacter globiformis anaerobically ...

ID or keywords:

Entry

Database: PDB / ID: 5zp4

Title

Copper amine oxidase from Arthrobacter globiformis anaerobically reduced by ethylamine at pH 10 at 288 K (2)

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 /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.799 Å

Authors

Murakawa, T. / Baba, S. / Kawano, Y. / Hayashi, H. / Yano, T. / Tanizawa, K. / Kumasaka, T. / Yamamoto, M. / Okajima, T.

Funding support

Japan, 1items

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: In crystallothermodynamic analysis of conformational change of the topaquinone cofactor in bacterial copper amine oxidase.
Authors: Murakawa, T. / Baba, S. / Kawano, Y. / Hayashi, H. / Yano, T. / Kumasaka, T. / Yamamoto, M. / Tanizawa, K. / Okajima, T.

History

Deposition	Apr 16, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 19, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 2, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Jan 16, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
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 / struct_conn_type 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.4	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5zp4.cif.gz	518.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5zp4_validation.pdf.gz	443.5 KB	Display	wwPDB validaton report
Full document	5zp4_full_validation.pdf.gz	449.4 KB	Display
Data in XML	5zp4_validation.xml.gz	54.2 KB	Display
Data in CIF	5zp4_validation.cif.gz	81.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zp/5zp4 ftp://data.pdbj.org/pub/pdb/validation_reports/zp/5zp4	HTTPS FTP

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Related structure data

Related structure data	5zouC 5zowC 5zoxC 5zoyC 5zozC 5zp0C 5zp1C 5zp2C 5zp3C 5zp5C 5zp6C 5zp7C 5zp8C 5zp9C 5zpaC 5zpbC 5zpcC 5zpdC 5zpeC 5zpfC 5zpgC 5zphC 5zpiC 5zpjC 5zpkC 5zplC 5zpmC 5zpnC 5zpoC 5zppC 5zpqC 5zprC 5zpsC 5zptC 1iu7S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1avk-1 5zp2-2 5zpc-d 5zoz-2 5zp9-d 3x42-d 1iqx-d 5zoy-2 5zpn-1 1ui8-d 5zpm-1 5zpo-2 5zpp-2 3x40-2 5zoz-1 1iu7-d 5zp5-2 5zp1-2 5zpl-2 3x3x-2 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

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phenylethylamine oxidase

B: Phenylethylamine oxidase

hetero molecules

138 kDa, 2 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: native gel electrophoresis
138 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Phenylethylamine oxidase

hetero molecules

B: Phenylethylamine oxidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	193.731, 64.838, 158.974
Angle α, β, γ (deg.)	90.00, 117.20, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-1136- HOH
2	1	A-1265- HOH
3	1	B-1090- HOH
4	1	B-1181- HOH

#1: Protein	Phenylethylamine oxidase / Primary amine oxidase Mass: 68913.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Plasmid: pepo-2 / Production host: Escherichia coli (E. coli) / Strain (production host): CD03 / References: UniProt: P46881, primary-amine oxidase
#2: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1004 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.22 Å³/Da / Density % sol: 61.82 %
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

Mean temperature: 288 K

Diffraction source

Source:

SYNCHROTRON / Site:

SPring-8

/ Beamline: BL38B1 / Wavelength: 1 Å

Detector

Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 1, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.799→50 Å / Num. obs: 162845 / % possible obs: 100 % / Redundancy: 3.7 % / B_iso Wilson estimate: 17.6 Å² / R_merge(I) obs: 0.088 / R_pim(I) all: 0.053 / R_rim(I) all: 0.102 / Χ²: 4.138 / Net I/σ(I): 10.1 / Num. measured all: 609475

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
1.8-1.83	3.7	0.43	8077	0.88	0.26	0.504	1.149	100
1.83-1.86	3.7	0.375	8114	0.903	0.226	0.439	1.171	100
1.86-1.9	3.8	0.32	8092	0.928	0.193	0.374	1.266	100
1.9-1.94	3.7	0.272	8068	0.944	0.164	0.318	1.317	100
1.94-1.98	3.8	0.235	8072	0.95	0.142	0.275	1.366	100
1.98-2.03	3.8	0.207	8154	0.964	0.124	0.242	1.521	100
2.03-2.08	3.8	0.186	8086	0.971	0.112	0.218	1.578	100
2.08-2.13	3.8	0.173	8078	0.971	0.104	0.202	1.592	100
2.13-2.2	3.8	0.154	8114	0.97	0.093	0.18	1.861	100
2.2-2.27	3.8	0.141	8113	0.98	0.084	0.165	1.871	100
2.27-2.35	3.8	0.131	8124	0.98	0.078	0.153	1.997	100
2.35-2.44	3.8	0.13	8151	0.977	0.078	0.152	2.418	100
2.44-2.55	3.8	0.129	8130	0.978	0.077	0.151	2.709	100
2.55-2.69	3.8	0.13	8166	0.976	0.078	0.152	3.504	100
2.69-2.86	3.8	0.125	8136	0.975	0.074	0.145	4.684	100
2.86-3.08	3.8	0.109	8145	0.979	0.065	0.127	5.941	100
3.08-3.39	3.7	0.079	8187	0.988	0.047	0.092	5.35	100
3.39-3.88	3.7	0.055	8179	0.992	0.033	0.064	6.987	100
3.88-4.88	3.7	0.046	8244	0.995	0.028	0.054	11.195	100
4.88-50	3.5	0.051	8415	0.989	0.032	0.06	24.111	99.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.24	data extraction
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1IU7

1iu7

Resolution: 1.799→35.135 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1681	8084	4.97 %
R_work	0.1447	-	-
obs	0.1459	162694	99.77 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.799→35.135 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9738	0	5	1004	10747

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	10227
X-RAY DIFFRACTION	f_angle_d	0.859	13998
X-RAY DIFFRACTION	f_dihedral_angle_d	7.148	8277
X-RAY DIFFRACTION	f_chiral_restr	0.061	1520
X-RAY DIFFRACTION	f_plane_restr	0.005	1867

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 (%)
1.7987-1.8192	0.2368	253	0.2311	4872	X-RAY DIFFRACTION	96
1.8192-1.8406	0.2115	276	0.2113	5129	X-RAY DIFFRACTION	100
1.8406-1.863	0.2633	280	0.2115	5153	X-RAY DIFFRACTION	100
1.863-1.8866	0.223	281	0.2008	5135	X-RAY DIFFRACTION	100
1.8866-1.9114	0.2343	289	0.1906	5100	X-RAY DIFFRACTION	100
1.9114-1.9376	0.2075	293	0.1766	5084	X-RAY DIFFRACTION	100
1.9376-1.9653	0.18	253	0.1659	5198	X-RAY DIFFRACTION	100
1.9653-1.9946	0.1869	279	0.1562	5089	X-RAY DIFFRACTION	100
1.9946-2.0258	0.195	250	0.1531	5195	X-RAY DIFFRACTION	100
2.0258-2.059	0.1823	277	0.1583	5074	X-RAY DIFFRACTION	100
2.059-2.0945	0.1809	246	0.1575	5205	X-RAY DIFFRACTION	100
2.0945-2.1326	0.1791	245	0.1531	5115	X-RAY DIFFRACTION	100
2.1326-2.1736	0.1729	288	0.1514	5189	X-RAY DIFFRACTION	100
2.1736-2.218	0.1834	258	0.1496	5154	X-RAY DIFFRACTION	100
2.218-2.2662	0.1736	256	0.1508	5122	X-RAY DIFFRACTION	100
2.2662-2.3189	0.1817	280	0.1502	5185	X-RAY DIFFRACTION	100
2.3189-2.3769	0.1607	250	0.1493	5149	X-RAY DIFFRACTION	100
2.3769-2.4411	0.1935	287	0.1549	5145	X-RAY DIFFRACTION	100
2.4411-2.5129	0.1893	266	0.1533	5135	X-RAY DIFFRACTION	100
2.5129-2.594	0.1807	289	0.1613	5178	X-RAY DIFFRACTION	100
2.594-2.6867	0.1696	269	0.1535	5170	X-RAY DIFFRACTION	100
2.6867-2.7942	0.1886	272	0.1558	5121	X-RAY DIFFRACTION	100
2.7942-2.9213	0.1726	274	0.1511	5184	X-RAY DIFFRACTION	100
2.9213-3.0753	0.1811	261	0.147	5195	X-RAY DIFFRACTION	100
3.0753-3.2678	0.1588	283	0.1356	5175	X-RAY DIFFRACTION	100
3.2678-3.5199	0.1426	290	0.1243	5175	X-RAY DIFFRACTION	100
3.5199-3.8737	0.1318	266	0.1098	5174	X-RAY DIFFRACTION	100
3.8737-4.4333	0.1302	267	0.1078	5233	X-RAY DIFFRACTION	100
4.4333-5.5819	0.12	281	0.1102	5224	X-RAY DIFFRACTION	100
5.5819-35.1413	0.165	225	0.1523	5353	X-RAY DIFFRACTION	98

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	1.4073	-0.4614	-1.0008	4.0085	0.2196	1.5372	0.0199	-0.027	0.0195	0.185	-0.1222	0.196	-0.1891	-0.367	0.0458	0.1663	0.04	0.0432	0.2023	-0.0675	0.1389	175.6438	24.3801	34.9146
2	0.401	0.0366	-0.088	0.2463	0.0027	1.3606	0.0003	-0.0709	0.0218	0.0433	-0.0135	-0.0003	-0.1116	-0.0205	0.0142	0.1078	0.0012	-0.0092	0.071	-0.0045	0.131	190.4657	17.1946	16.8421
3	1.7639	-0.3262	0.5341	0.2314	-0.0803	1.2041	-0.0262	0.0849	0.098	-0.0012	-0.0144	-0.0128	-0.1763	0.0017	0.0456	0.1	0.0022	-0.0121	0.0661	-0.0083	0.1125	189.3161	19.4817	4.4352
4	1.3032	0.186	-1.1268	4.2944	-0.003	2.3682	-0.0058	0.0291	-0.0235	-0.1023	-0.0115	-0.2326	-0.0556	0.3789	-0.0023	0.0975	-0.0182	0.0544	0.1445	0.0395	0.1369	177.3563	-7.4907	36.6897
5	0.9306	0.0561	-0.0908	0.3562	0.0018	0.8257	0.0006	0.3148	-0.062	-0.1056	-0.0046	-0.0095	-0.0432	-0.2308	0.0222	0.1651	0.0256	-0.0248	0.1745	0.0153	0.1399	149.8597	-13.6651	37.8277
6	0.2918	-0.1121	-0.1264	0.2481	0.0049	1.0576	0.0448	0.0199	0.0387	-0.0392	-0.0147	-0.0119	-0.2377	0.0639	-0.0161	0.1481	-0.0189	0.0005	0.0814	-0.001	0.1364	165.3971	-5.2371	59.007
7	0.3724	-0.0651	-0.0348	0.2964	-0.0381	1.1045	-0.0115	0.0117	-0.035	-0.013	0.0063	-0.0209	0.0918	0.1296	-0.0008	0.0921	0.0096	-0.0042	0.0716	-0.0014	0.1295	165.9654	-22.5695	62.9411

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 72 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 73 through 581 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 582 through 628 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 9 through 72 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 73 through 225 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 226 through 402 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 403 through 628 )

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