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

ID or keywords:

Entry

Database: PDB / ID: 5zpo

Title

Copper amine oxidase from Arthrobacter globiformis anaerobically reduced by phenylethylamine at pH 8 at 288 K (2)

Components

Phenylethylamine oxidase

Keywords

OXIDOREDUCTASE / COPPER AMINE OXIDASE /

TOPAQUINONE / TPQ

Function / homology

Function and homology information

: / : / : /

primary-amine oxidase / amine metabolic process /

quinone binding / copper ion binding
Similarity search - Function

Biological species

Arthrobacter globiformis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.73 Å

Authors

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

Funding support

Japan, 6items

Organization	Grant number	Country
Japan Agency for Medical Research and Development (AMED)	0294	Japan
Japan Society for the Promotion of Science	17K07317	Japan
Japan Society for the Promotion of Science	JP26440037	Japan
Japan Society for the Promotion of Science	JP23770127	Japan
Japan Society for the Promotion of Science	JP15K05573	Japan
Japan Society for the Promotion of Science	JP16KT0055	Japan

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 23, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5zpo.cif.gz	526.8 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zp/5zpo ftp://data.pdbj.org/pub/pdb/validation_reports/zp/5zpo	HTTPS FTP

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Related structure data

Related structure data	5zouC 5zowC 5zoxC 5zoyC 5zozC 5zp0C 5zp1C 5zp2C 5zp3C 5zp4C 5zp5C 5zp6C 5zp7C 5zp8C 5zp9C 5zpaC 5zpbC 5zpcC 5zpdC 5zpeC 5zpfC 5zpgC 5zphC 5zpiC 5zpjC 5zpkC 5zplC 5zpmC 5zpnC 5zppC 5zpqC 5zprC 5zpsC 5zptC 1iu7S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5zpf-d 1avl-1 5zp1-1 5zp5-1 5zp8-d 2e2t-1 5zpd-d 2yx9-d 5zpr-2 5zp7-d 1wmn-d 1rjo-1 1ivw-d 5zpp-1 1wmo-d 5zpk-1 5zpm-2 5zps-2 5zpe-d 1sih-1 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)	192.997, 64.684, 158.918
Angle α, β, γ (deg.)	90.00, 117.01, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-1102- HOH
2	1	A-1183- HOH
3	1	B-1187- HOH
4	1	B-1234- HOH

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 1037 molecules

#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-HY1 / PHENYLACETALDEHYDE / Phenylacetaldehyde Mass: 120.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₈O
#5: Chemical	ChemComp-CU / COPPER (II) ION / Copper Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1028 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.21 Å³/Da / Density % sol: 61.63 %
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: 1.72→50 Å / Num. obs: 187338 / % possible obs: 100 % / Redundancy: 4.2 % / B_iso Wilson estimate: 18.3 Å² / R_merge(I) obs: 0.095 / R_pim(I) all: 0.053 / R_rim(I) all: 0.109 / Χ²: 3.115 / Net I/σ(I): 7.9 / Num. measured all: 780754

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
1.72-1.75	4.1	0.784	9342	0.732	0.44	0.901	0.97	100
1.75-1.78	4.2	0.653	9292	0.789	0.363	0.749	1.005	100
1.78-1.82	4.2	0.543	9290	0.845	0.301	0.622	1.021	100
1.82-1.85	4.2	0.473	9363	0.873	0.262	0.542	1.079	100
1.85-1.89	4.2	0.382	9305	0.911	0.212	0.438	1.081	100
1.89-1.94	4.2	0.315	9294	0.94	0.175	0.361	1.129	100
1.94-1.99	4.2	0.262	9313	0.955	0.146	0.301	1.178	100
1.99-2.04	4.2	0.22	9350	0.969	0.122	0.252	1.234	100
2.04-2.1	4.2	0.198	9339	0.969	0.11	0.227	1.357	100
2.1-2.17	4.2	0.174	9348	0.974	0.096	0.199	1.379	100
2.17-2.24	4.2	0.15	9337	0.982	0.083	0.171	1.365	100
2.24-2.33	4.2	0.135	9347	0.982	0.075	0.155	1.548	100
2.33-2.44	4.2	0.129	9323	0.984	0.071	0.147	1.643	100
2.44-2.57	4.2	0.129	9369	0.982	0.071	0.148	2.137	100
2.57-2.73	4.2	0.126	9367	0.981	0.07	0.144	2.823	100
2.73-2.94	4.2	0.117	9413	0.978	0.065	0.133	3.985	100
2.94-3.24	4.2	0.095	9403	0.985	0.053	0.109	4.573	100
3.24-3.71	4.2	0.064	9421	0.988	0.035	0.073	7.088	100
3.71-4.67	4.1	0.046	9479	0.994	0.025	0.052	6.984	100
4.67-50	4	0.048	9643	0.989	0.027	0.055	19.232	99.7

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Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	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: 1.73→35.4 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.31 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.162	8964	4.93 %
R_work	0.14	-	-
obs	0.141	181898	99.7 %

Solvent computation

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

Displacement parameters

B_iso mean: 25.72 Å²

Refinement step

Cycle: LAST / Resolution: 1.73→35.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9738	0	31	1028	10797

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	10390
X-RAY DIFFRACTION	f_angle_d	0.941	14229
X-RAY DIFFRACTION	f_dihedral_angle_d	16.756	6238
X-RAY DIFFRACTION	f_chiral_restr	0.062	1537
X-RAY DIFFRACTION	f_plane_restr	0.005	1900

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 (%)
1.7294-1.749	0.2341	267	0.2282	5322	X-RAY DIFFRACTION	92
1.749-1.7696	0.2353	296	0.2146	5681	X-RAY DIFFRACTION	100
1.7696-1.7912	0.2297	298	0.2077	5797	X-RAY DIFFRACTION	100
1.7912-1.8138	0.2149	307	0.2	5716	X-RAY DIFFRACTION	100
1.8138-1.8377	0.2207	291	0.1948	5753	X-RAY DIFFRACTION	100
1.8377-1.8629	0.232	281	0.1918	5786	X-RAY DIFFRACTION	100
1.8629-1.8895	0.2087	282	0.1838	5778	X-RAY DIFFRACTION	100
1.8895-1.9177	0.2011	289	0.1718	5758	X-RAY DIFFRACTION	100
1.9177-1.9477	0.1925	299	0.163	5734	X-RAY DIFFRACTION	100
1.9477-1.9796	0.164	305	0.1528	5755	X-RAY DIFFRACTION	100
1.9796-2.0137	0.1797	294	0.1497	5758	X-RAY DIFFRACTION	100
2.0137-2.0503	0.1701	298	0.1459	5755	X-RAY DIFFRACTION	100
2.0503-2.0898	0.1685	311	0.1483	5759	X-RAY DIFFRACTION	100
2.0898-2.1324	0.172	328	0.1435	5716	X-RAY DIFFRACTION	100
2.1324-2.1788	0.1619	316	0.1397	5752	X-RAY DIFFRACTION	100
2.1788-2.2295	0.1693	299	0.1414	5781	X-RAY DIFFRACTION	100
2.2295-2.2852	0.1659	267	0.144	5754	X-RAY DIFFRACTION	100
2.2852-2.347	0.1661	305	0.1439	5778	X-RAY DIFFRACTION	100
2.347-2.416	0.1797	307	0.1481	5806	X-RAY DIFFRACTION	100
2.416-2.494	0.1902	345	0.1538	5728	X-RAY DIFFRACTION	100
2.494-2.5831	0.1908	292	0.151	5805	X-RAY DIFFRACTION	100
2.5831-2.6865	0.1853	301	0.1529	5781	X-RAY DIFFRACTION	100
2.6865-2.8087	0.1682	282	0.1537	5797	X-RAY DIFFRACTION	100
2.8087-2.9567	0.1684	299	0.1452	5764	X-RAY DIFFRACTION	100
2.9567-3.1419	0.1647	313	0.1385	5792	X-RAY DIFFRACTION	100
3.1419-3.3843	0.152	298	0.127	5843	X-RAY DIFFRACTION	100
3.3843-3.7245	0.1303	293	0.1084	5812	X-RAY DIFFRACTION	100
3.7245-4.2627	0.114	317	0.1027	5845	X-RAY DIFFRACTION	100
4.2627-5.3675	0.1122	281	0.099	5896	X-RAY DIFFRACTION	100
5.3675-35.4025	0.1536	303	0.1407	5932	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	1.0696	-0.261	-1.1677	4.3256	-0.2831	2.0362	0.0202	-0.0129	0.0204	0.1263	-0.0933	0.212	-0.2341	-0.383	0.0368	0.1668	0.0551	0.0384	0.232	-0.0694	0.1563	175.188	29.024	34.796
2	0.3509	0.0244	-0.0475	0.2156	-0.0058	1.223	-0.0033	-0.0605	0.0225	0.0351	-0.0071	-0.0084	-0.1381	-0.0067	0.0136	0.1211	0.0019	-0.0029	0.089	-0.0048	0.1425	191.029	23.673	16.643
3	0.8388	-0.1004	0.2588	0.179	0.0169	1.2697	-0.0086	-0.049	-0.0185	0.0301	-0.0092	0.0248	0.0158	-0.1531	0.0105	0.1026	-0.0005	0.0017	0.0897	-0.0082	0.1295	184.825	15.975	12.908
4	0.9311	0.0806	-1.1681	4.5532	0.1514	2.6807	-0.0092	-0.0048	0.0105	-0.097	-0.0231	-0.1935	-0.0658	0.3234	-0.0214	0.0939	-0.0084	0.0516	0.1834	0.0378	0.1423	176.641	-2.834	36.985
5	2.0409	0.02	-0.2298	0.252	-0.0166	0.699	-0.0164	0.3862	-0.0642	-0.1171	0.0058	0.007	-0.0149	-0.1596	0.009	0.1696	0.0157	-0.0138	0.2129	-0.0151	0.1378	151.941	-12.557	33.116
6	0.3339	-0.0541	-0.0937	0.2823	-0.0141	1.0246	0.0145	0.0167	-0.0021	-0.0215	-0.0068	-0.0038	-0.0716	0.0687	-0.0041	0.1034	-0.0017	0.0004	0.0819	-0.0008	0.1336	163.505	-9.177	60.199
7	2.0473	0.2963	0.8559	0.2077	0.1519	1.3215	-0.0254	-0.065	0.0811	0.0021	-0.0103	0.0003	-0.1212	0.0068	0.038	0.1015	-0.0054	0.0014	0.0774	0.0113	0.1247	161.499	-7.73	66.607

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 516 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 517 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 191 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 192 THROUGH 581 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 582 THROUGH 628 )

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