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

ID or keywords:

Entry

Database: PDB / ID: 5zpm

Title

Copper amine oxidase from Arthrobacter globiformis anaerobically reduced by phenylethylamine at pH 7 at 288 K (2)

Components

Phenylethylamine oxidase

Keywords

OXIDOREDUCTASE / COPPER AMINE OXIDASE / TOPAQUINONE / TPQ

Function / homology

Function and homology information

primary-amine oxidase / 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: 1.65 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	Feb 13, 2019	Group: Data collection / Database references / Category: citation 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
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
Revision 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5zpm.cif.gz	529.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5zpm_validation.pdf.gz	454.9 KB	Display	wwPDB validaton report
Full document	5zpm_full_validation.pdf.gz	459.9 KB	Display
Data in XML	5zpm_validation.xml.gz	54.8 KB	Display
Data in CIF	5zpm_validation.cif.gz	81.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zp/5zpm ftp://data.pdbj.org/pub/pdb/validation_reports/zp/5zpm	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 5zpnC 5zpoC 5zppC 5zpqC 5zprC 5zpsC 5zptC 1iu7S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5zoy-2 1wmp-d 5zpn-1 1iu7-d 5zpc-d 5zp4-1 5zou-d 5zpp-2 5zp2-2 5zp3-1 1ui8-d 5zpq-2 5zp9-d 5zp1-2 5zps-1 5zpo-2 2cwv-d 5zpg-d 5zpt-1 3x42-d 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)	192.866, 64.320, 158.903
Angle α, β, γ (deg.)	90.00, 116.92, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-1100- HOH
2	1	A-1218- HOH
3	1	B-1188- HOH
4	1	B-1191- HOH
5	1	B-1306- HOH

#1: Protein	Phenylethylamine oxidase / Primary amine oxidase Mass: 69015.883 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-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 Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1018 / 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: 3.18 Å³/Da / Density % sol: 61.36 %
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: Nov 8, 2015

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.65→50 Å / Num. obs: 208626 / % possible obs: 99.9 % / Redundancy: 3.7 % / B_iso Wilson estimate: 17.39 Å² / R_merge(I) obs: 0.086 / R_pim(I) all: 0.053 / R_rim(I) all: 0.101 / Χ²: 1.741 / Net I/σ(I): 8.6

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
1.65-1.68	3.6	0.68	10332	0.745	0.418	0.8	0.968	99.9
1.68-1.71	3.7	0.59	10382	0.795	0.359	0.692	0.978	100
1.71-1.74	3.7	0.548	10378	0.825	0.332	0.642	1.017	100
1.74-1.78	3.7	0.457	10408	0.862	0.276	0.536	1.049	100
1.78-1.82	3.7	0.379	10371	0.901	0.229	0.444	1.091	100
1.82-1.86	3.7	0.332	10388	0.916	0.2	0.388	1.141	100
1.86-1.9	3.7	0.268	10364	0.946	0.161	0.313	1.214	100
1.9-1.96	3.7	0.222	10449	0.959	0.134	0.26	1.293	100
1.96-2.01	3.7	0.187	10368	0.97	0.112	0.218	1.4	100
2.01-2.08	3.7	0.163	10400	0.977	0.098	0.191	1.448	100
2.08-2.15	3.7	0.149	10395	0.978	0.09	0.175	1.556	100
2.15-2.24	3.7	0.131	10404	0.983	0.079	0.153	1.638	99.9
2.24-2.34	3.7	0.121	10395	0.985	0.072	0.141	1.786	100
2.34-2.46	3.7	0.118	10463	0.985	0.071	0.137	1.996	99.9
2.46-2.62	3.7	0.114	10416	0.985	0.069	0.133	2.36	100
2.62-2.82	3.7	0.102	10492	0.988	0.062	0.12	2.725	100
2.82-3.11	3.6	0.086	10445	0.99	0.053	0.101	3.136	100
3.11-3.55	3.7	0.063	10485	0.995	0.039	0.075	3.069	100
3.55-4.48	3.7	0.046	10547	0.997	0.028	0.054	2.732	99.8
4.48-50	3.5	0.035	10744	0.998	0.022	0.042	2.302	99.6

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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: 1.65→36.675 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.72

	R_factor	Num. reflection	% reflection
R_free	0.1712	10332	4.96 %
R_work	0.1485	-	-
obs	0.1497	208506	99.68 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.65→36.675 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9754	0	17	1018	10789

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	10396
X-RAY DIFFRACTION	f_angle_d	0.872	14230
X-RAY DIFFRACTION	f_dihedral_angle_d	6.958	9434
X-RAY DIFFRACTION	f_chiral_restr	0.06	1535
X-RAY DIFFRACTION	f_plane_restr	0.005	1898

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 (%)
1.649-1.6677	0.2921	326	0.2719	6147	X-RAY DIFFRACTION	93
1.6677-1.6873	0.2585	327	0.2572	6585	X-RAY DIFFRACTION	100
1.6873-1.7079	0.277	366	0.2445	6532	X-RAY DIFFRACTION	100
1.7079-1.7295	0.2694	344	0.2338	6619	X-RAY DIFFRACTION	100
1.7295-1.7523	0.2482	353	0.2257	6617	X-RAY DIFFRACTION	100
1.7523-1.7763	0.2355	316	0.2058	6585	X-RAY DIFFRACTION	100
1.7763-1.8016	0.2228	317	0.1918	6600	X-RAY DIFFRACTION	100
1.8016-1.8285	0.1796	357	0.1803	6587	X-RAY DIFFRACTION	100
1.8285-1.8571	0.1914	341	0.1709	6596	X-RAY DIFFRACTION	100
1.8571-1.8876	0.1846	323	0.1683	6641	X-RAY DIFFRACTION	100
1.8876-1.9201	0.1904	333	0.1598	6580	X-RAY DIFFRACTION	100
1.9201-1.955	0.1853	359	0.1565	6608	X-RAY DIFFRACTION	100
1.955-1.9926	0.1782	358	0.1562	6606	X-RAY DIFFRACTION	100
1.9926-2.0333	0.1717	331	0.1533	6604	X-RAY DIFFRACTION	100
2.0333-2.0775	0.1675	386	0.1456	6577	X-RAY DIFFRACTION	100
2.0775-2.1258	0.1786	364	0.144	6528	X-RAY DIFFRACTION	100
2.1258-2.179	0.1615	350	0.1417	6605	X-RAY DIFFRACTION	100
2.179-2.2379	0.1598	333	0.1419	6635	X-RAY DIFFRACTION	100
2.2379-2.3037	0.1753	318	0.1464	6670	X-RAY DIFFRACTION	100
2.3037-2.3781	0.1665	356	0.1442	6617	X-RAY DIFFRACTION	100
2.3781-2.463	0.1814	343	0.1531	6586	X-RAY DIFFRACTION	100
2.463-2.5616	0.1722	345	0.1535	6635	X-RAY DIFFRACTION	100
2.5616-2.6782	0.1737	340	0.1588	6685	X-RAY DIFFRACTION	100
2.6782-2.8193	0.1947	326	0.1611	6620	X-RAY DIFFRACTION	100
2.8193-2.9959	0.178	351	0.1539	6638	X-RAY DIFFRACTION	100
2.9959-3.2271	0.1666	347	0.1426	6649	X-RAY DIFFRACTION	100
3.2271-3.5516	0.1456	356	0.1231	6643	X-RAY DIFFRACTION	100
3.5516-4.065	0.1325	365	0.1111	6690	X-RAY DIFFRACTION	100
4.065-5.1192	0.1239	357	0.1056	6701	X-RAY DIFFRACTION	100
5.1192-36.6842	0.1763	344	0.15	6788	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	1.6115	0.0027	-0.898	2.1087	0.35	0.5592	0.1205	-0.12	0.1049	0.3574	-0.1908	0.0994	-0.2424	-0.2152	0.0262	0.2774	0.0342	0.0383	0.2694	-0.0728	0.1613	-16.266	18.374	36.484
2	1.6627	0.794	-1.3564	4.0469	0.6852	2.2572	0.0071	-0.1626	-0.0125	0.201	-0.1196	0.4981	-0.2529	-0.5332	-0.0295	0.1687	0.008	0.0628	0.3005	-0.0869	0.1934	-19.67	9.768	35.104
3	3.6344	0.6666	1.2121	0.2392	0.3781	0.6798	-0.0044	-0.4607	0.0586	0.1559	-0.0328	-0.0398	-0.0117	0.1539	0.0574	0.1971	-0.0415	-0.033	0.3582	0.0073	0.1641	13.329	7.939	39.027
4	0.9089	-0.1095	0.1675	0.3367	-0.184	1.2048	-0.0067	-0.1541	0.0368	0.0641	-0.0119	-0.0096	-0.1959	0.0291	0.0147	0.1647	-0.0187	-0.0084	0.1089	-0.0385	0.1245	1.837	13.614	21.052
5	0.2956	0.0677	-0.0144	0.2827	0.0112	1.0831	0.0039	-0.0143	-0.0021	0.0158	-0.0122	0.007	-0.0821	-0.0749	0.0107	0.0933	0.008	-0.0055	0.1063	-0.0023	0.1187	-5.389	8.211	8.386
6	0.7303	-0.0474	0.2112	0.2264	0.0251	1.1161	0.0102	-0.0788	-0.0102	0.0392	-0.0137	0.0301	0.0119	-0.1409	-0.0049	0.0911	-0.0078	-0.0005	0.1034	-0.0074	0.1119	-8.201	2.146	12.883
7	0.7706	-0.0286	-0.5459	1.252	-0.4413	2.0091	0.0113	0.0871	0.0321	-0.171	0.0266	-0.0415	-0.1329	0.3226	-0.0438	0.1844	-0.0276	0.0325	0.2256	0.0321	0.1642	-17.992	-13.429	35.085
8	1.7548	-0.4713	-1.1725	4.1199	-0.8494	2.4502	-0.08	0.0398	-0.1295	-0.1396	0.0358	-0.4461	-0.0877	0.4824	-0.1028	0.1113	0.0205	0.053	0.2052	0.0191	0.1524	-14.746	-22.088	36.609
9	2.3683	-0.3074	0.2569	0.4836	-0.2971	1.222	0.0001	0.4441	-0.0843	-0.1429	-0.0025	-0.0202	0.0212	-0.1054	0.0014	0.1655	0.0024	-0.0239	0.2327	-0.021	0.132	-46.742	-26.708	33.165
10	0.7285	0.0516	0.1114	0.3524	0.1529	1.0189	0.0142	0.0294	0.0832	-0.0275	0.007	0.0065	-0.2248	0.045	-0.0144	0.1681	-0.0093	-0.001	0.065	0.0232	0.1315	-31.244	-11.476	59.126
11	0.2694	-0.0529	-0.0803	0.2581	-0.0082	0.8845	0.0128	0.0084	-0.0151	-0.0137	0.0005	-0.0087	-0.0443	0.0504	-0.011	0.11	-0.0042	-0.0044	0.1031	-0.0022	0.1347	-30.239	-23.552	62.679
12	0.6347	0.0682	0.1698	0.1924	-0.0272	0.9756	0.0108	0.0596	-0.0268	-0.0347	-0.0084	-0.0367	0.048	0.1179	-0.0056	0.1097	0.0103	-0.0015	0.1011	0.0023	0.1333	-27.253	-29.574	58.335

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 44 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 45 through 95 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 96 through 138 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 139 through 277 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 278 through 516 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 517 through 628 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 9 through 44 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 45 through 95 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 96 through 191 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 192 through 277 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 278 through 516 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 517 through 628 )

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi