PDB-5zp1: Copper amine oxidase from Arthrobacter globiformis anaerobically ...

ID or keywords:

Entry

Database: PDB / ID: 5zp1

Title

Copper amine oxidase from Arthrobacter globiformis anaerobically reduced by ethylamine at pH 9 at 288 K (1)

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: 1.669 Å

Authors

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

Funding support

Japan, 2items

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

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zp/5zp1 ftp://data.pdbj.org/pub/pdb/validation_reports/zp/5zp1	HTTPS FTP

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Related structure data

Related structure data	5zouC 5zowC 5zoxC 5zoyC 5zozC 5zp0C 5zp2C 5zp3C 5zp4C 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	5zpf-d 2yx9-d 1rjo-1 5zp8-d 1sih-1 5zps-1 5zp7-d 5zp5-1 5zpp-1 5zpo-1 2d1w-d 5zps-2 1avl-1 1ivv-d 2e2t-1 5zpg-d 2cfl-1 5zpk-1 5zpd-d 5zpr-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)	193.665, 64.739, 158.920
Angle α, β, γ (deg.)	90.00, 117.16, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-1096- 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 / Copper 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: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1023 / 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: 3.22 Å³/Da / Density % sol: 61.75 %
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: 1.67→50 Å / Num. obs: 200673 / % possible obs: 98.7 % / Redundancy: 4.2 % / B_iso Wilson estimate: 18 Å² / R_merge(I) obs: 0.07 / R_pim(I) all: 0.039 / R_rim(I) all: 0.081 / Χ²: 1.468 / Net I/σ(I): 9.5 / Num. measured all: 839213

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
1.67-1.7	4.1	0.653	9859	0.794	0.367	0.751	0.954	97.4
1.7-1.73	4.2	0.606	9846	0.837	0.334	0.693	0.981	97.7
1.73-1.76	4.2	0.523	9853	0.875	0.286	0.598	1.007	97.9
1.76-1.8	4.2	0.426	9917	0.907	0.233	0.487	1.044	98
1.8-1.84	4.2	0.356	9886	0.93	0.195	0.406	1.094	98.1
1.84-1.88	4.2	0.301	9963	0.946	0.165	0.344	1.132	98.2
1.88-1.93	4.2	0.24	9956	0.964	0.132	0.274	1.175	98.4
1.93-1.98	4.2	0.202	9917	0.973	0.111	0.231	1.252	98.4
1.98-2.04	4.2	0.171	10038	0.981	0.094	0.195	1.336	98.5
2.04-2.1	4.2	0.151	9972	0.984	0.083	0.172	1.361	98.8
2.1-2.18	4.2	0.134	9998	0.985	0.074	0.153	1.404	98.7
2.18-2.27	4.2	0.116	10034	0.989	0.064	0.132	1.461	99
2.27-2.37	4.2	0.105	10070	0.99	0.058	0.121	1.527	99.1
2.37-2.49	4.2	0.101	10131	0.99	0.056	0.116	1.672	99.2
2.49-2.65	4.2	0.097	10016	0.99	0.054	0.111	1.998	99.3
2.65-2.86	4.1	0.085	10171	0.992	0.048	0.098	2.279	99.4
2.86-3.14	4.1	0.07	10130	0.994	0.039	0.08	2.445	99.6
3.14-3.6	4.1	0.048	10224	0.997	0.027	0.055	2.067	99.7
3.6-4.53	4.1	0.035	10221	0.998	0.02	0.04	1.712	99.8
4.53-50	3.9	0.027	10471	0.999	0.016	0.031	1.431	99.5

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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: 1.669→40.489 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.06 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1656	9765	4.87 %
R_work	0.1457	-	-
obs	0.1467	200580	98.56 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.669→40.489 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9738	0	17	1023	10778

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	10214
X-RAY DIFFRACTION	f_angle_d	0.867	13967
X-RAY DIFFRACTION	f_dihedral_angle_d	6.269	8263
X-RAY DIFFRACTION	f_chiral_restr	0.061	1514
X-RAY DIFFRACTION	f_plane_restr	0.005	1862

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 (%)
1.669-1.6879	0.2655	320	0.2587	5915	X-RAY DIFFRACTION	93
1.6879-1.7078	0.2702	309	0.2463	6318	X-RAY DIFFRACTION	98
1.7078-1.7286	0.2766	316	0.2408	6275	X-RAY DIFFRACTION	98
1.7286-1.7505	0.2519	329	0.2272	6270	X-RAY DIFFRACTION	98
1.7505-1.7735	0.232	348	0.2097	6207	X-RAY DIFFRACTION	98
1.7735-1.7978	0.2254	303	0.1987	6357	X-RAY DIFFRACTION	98
1.7978-1.8235	0.215	314	0.1942	6270	X-RAY DIFFRACTION	98
1.8235-1.8507	0.2296	338	0.1867	6323	X-RAY DIFFRACTION	98
1.8507-1.8797	0.192	291	0.1827	6309	X-RAY DIFFRACTION	98
1.8797-1.9105	0.1896	316	0.1753	6336	X-RAY DIFFRACTION	98
1.9105-1.9434	0.1811	325	0.1626	6281	X-RAY DIFFRACTION	98
1.9434-1.9788	0.1772	303	0.1541	6342	X-RAY DIFFRACTION	98
1.9788-2.0168	0.1919	326	0.1508	6394	X-RAY DIFFRACTION	99
2.0168-2.058	0.2106	309	0.1539	6295	X-RAY DIFFRACTION	99
2.058-2.1027	0.1838	354	0.1504	6354	X-RAY DIFFRACTION	99
2.1027-2.1516	0.1849	325	0.1453	6312	X-RAY DIFFRACTION	99
2.1516-2.2054	0.1736	341	0.1458	6373	X-RAY DIFFRACTION	99
2.2054-2.2651	0.1698	314	0.1451	6393	X-RAY DIFFRACTION	99
2.2651-2.3317	0.1624	351	0.1449	6401	X-RAY DIFFRACTION	99
2.3317-2.407	0.1795	334	0.1507	6371	X-RAY DIFFRACTION	99
2.407-2.493	0.1749	317	0.151	6450	X-RAY DIFFRACTION	99
2.493-2.5928	0.1671	318	0.1551	6411	X-RAY DIFFRACTION	99
2.5928-2.7108	0.1804	298	0.1527	6418	X-RAY DIFFRACTION	99
2.7108-2.8536	0.1743	356	0.155	6412	X-RAY DIFFRACTION	99
2.8536-3.0324	0.159	336	0.1484	6406	X-RAY DIFFRACTION	100
3.0324-3.2664	0.1728	304	0.1393	6532	X-RAY DIFFRACTION	100
3.2664-3.5949	0.1311	343	0.1186	6474	X-RAY DIFFRACTION	100
3.5949-4.1147	0.1263	352	0.1059	6457	X-RAY DIFFRACTION	100
4.1147-5.1824	0.1139	346	0.1004	6527	X-RAY DIFFRACTION	100
5.1824-40.5004	0.1381	329	0.1404	6632	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	1.1608	-0.1186	-1.1775	4.5665	-0.2844	1.9568	0.0398	-0.0178	0.0355	0.1357	-0.098	0.2489	-0.2209	-0.4127	0.0112	0.1529	0.0452	0.0364	0.2237	-0.0696	0.144	175.6157	24.1372	34.8435
2	0.3933	0.0524	-0.1005	0.256	-0.0132	1.3364	-0.0008	-0.0655	0.0153	0.0395	-0.0111	-0.0045	-0.1099	-0.0315	0.0135	0.1074	0.0025	-0.0092	0.084	-0.0045	0.133	190.4115	17.1836	15.8281
3	1.2349	-0.026	-1.4597	4.9221	0.0555	2.4654	-0.0179	-0.0335	0.0042	-0.0601	0.0076	-0.2297	-0.0751	0.3693	-0.0328	0.0811	-0.014	0.0489	0.1511	0.0328	0.1344	177.383	-7.6582	36.8663
4	5.4205	2.5678	0.7365	1.3586	0.7169	1.2853	-0.0712	0.3587	0.3333	-0.0851	0.0309	-0.1078	-0.0566	0.0226	0.0519	0.1923	0.0139	0.0375	0.1438	0.0242	0.1226	167.4858	-14.4285	32.3694
5	0.3682	-0.043	-0.1034	0.2312	-0.0099	1.0117	0.0129	0.0471	-0.0065	-0.0307	-0.0017	0.0019	-0.0612	0.0189	-0.0057	0.1039	0.0018	-0.004	0.0769	-0.0013	0.1312	161.1094	-14.6136	56.8378

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 628 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 9 through 72 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 73 through 114 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 115 through 628 )

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