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

ID or keywords:

Entry

Database: PDB / ID: 5zpj

Title

Copper amine oxidase from Arthrobacter globiformis anaerobically reduced by phenylethylamine at pH 6 at 288 K (1)

Components

Phenylethylamine oxidase

Keywords

SPLICING / COPPER AMINE OXIDASE / TOPAQUINONE / TPQ / OXIDOREDUCTASE

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: 1.647 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5zpj.cif.gz	524.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5zpj_validation.pdf.gz	460.3 KB	Display	wwPDB validaton report
Full document	5zpj_full_validation.pdf.gz	466 KB	Display
Data in XML	5zpj_validation.xml.gz	54.2 KB	Display
Data in CIF	5zpj_validation.cif.gz	81.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zp/5zpj ftp://data.pdbj.org/pub/pdb/validation_reports/zp/5zpj	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 5zpkC 5zplC 5zpmC 5zpnC 5zpoC 5zppC 5zpqC 5zprC 5zpsC 5zptC 1iu7S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3wa3-2 1ui7-d 3x40-2 1wmp-d 5zp5-2 5zpq-2 5zpe-d 5zpi-d 5zpk-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phenylethylamine oxidase

B: Phenylethylamine oxidase

hetero molecules

139 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
139 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)	192.960, 64.597, 158.901
Angle α, β, γ (deg.)	90.000, 116.890, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-1188- HOH
2	1	A-1221- HOH
3	1	B-1210- HOH
4	1	B-1228- HOH
5	1	B-1274- HOH

#1: Protein	Phenylethylamine oxidase / Primary amine oxidase Mass: 69015.883 Da / Num. of mol.: 2 / Fragment: UNP residues 9-628 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: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 996 / 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: 3.2 Å³/Da / Density % sol: 61.56 %
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: 210429 / % possible obs: 99.9 % / Redundancy: 3.7 % / R_merge(I) obs: 0.086 / R_pim(I) all: 0.052 / R_rim(I) all: 0.098 / Χ²: 1.555 / Net I/σ(I): 7.8 / Num. measured all: 786257

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	Χ²	% possible all	R_rim(I) all
1.65-1.68	3.6	0.855	10375	0.641	0.525	0.99	99.7
1.68-1.71	3.7	0.761	10498	0.712	0.462	1.014	100	0.892
1.71-1.74	3.7	0.696	10468	0.75	0.419	1.026	100	0.814
1.74-1.78	3.8	0.585	10466	0.798	0.35	1.061	100	0.683
1.78-1.82	3.8	0.487	10465	0.847	0.292	1.119	100	0.569
1.82-1.86	3.8	0.414	10507	0.88	0.248	1.135	100	0.484
1.86-1.9	3.8	0.334	10498	0.923	0.199	1.188	100	0.39
1.9-1.96	3.8	0.27	10500	0.944	0.162	1.25	100	0.316
1.96-2.01	3.8	0.219	10471	0.96	0.131	1.32	99.9	0.255
2.01-2.08	3.8	0.189	10521	0.971	0.113	1.352	100	0.22
2.08-2.15	3.8	0.171	10473	0.972	0.102	1.411	100	0.2
2.15-2.24	3.8	0.146	10491	0.979	0.087	1.465	100	0.17
2.24-2.34	3.8	0.13	10492	0.983	0.077	1.553	100	0.151
2.34-2.46	3.8	0.123	10506	0.985	0.074	1.692	99.9	0.144
2.46-2.62	3.8	0.116	10553	0.985	0.07	1.966	100	0.136
2.62-2.82	3.7	0.103	10551	0.987	0.062	2.328	99.9	0.121
2.82-3.11	3.7	0.085	10555	0.991	0.052	2.671	99.9	0.1
3.11-3.55	3.7	0.062	10575	0.994	0.038	2.652	99.9	0.073
3.55-4.48	3.7	0.041	10635	0.997	0.025	2.123	99.8	0.048
4.48-50	3.5	0.031	10829	0.999	0.019	1.772	99.6	0.037

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.10.1_2155	refinement
PDB_EXTRACT	3.24	data extraction
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1iu7

1iu7

Resolution: 1.647→35.43 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 18.88 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1753	10441	4.96 %
R_work	0.1543	199895	-
obs	0.1554	210336	99.67 %

Solvent computation

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

Displacement parameters

B_iso max: 194.47 Å² / B_iso mean: 22.6607 Å² / B_iso min: 5.65 Å²

Refinement step

Cycle: final / Resolution: 1.647→35.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9754	0	25	996	10775
B_iso mean	-	-	39.2	35.68	-
Num. residues	-	-	-	-	1240

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	10289
X-RAY DIFFRACTION	f_angle_d	0.88	14066
X-RAY DIFFRACTION	f_chiral_restr	0.061	1523
X-RAY DIFFRACTION	f_plane_restr	0.006	1878
X-RAY DIFFRACTION	f_dihedral_angle_d	17.132	6161

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6468-1.6655	0.3305	346	0.3147	6174	6520	93
1.6655-1.6851	0.3117	324	0.2959	6621	6945	100
1.6851-1.7057	0.2929	361	0.2749	6639	7000	100
1.7057-1.7273	0.2942	321	0.2627	6641	6962	100
1.7273-1.75	0.2785	366	0.2576	6700	7066	100
1.75-1.774	0.2669	323	0.2425	6628	6951	100
1.774-1.7993	0.2475	340	0.2386	6658	6998	100
1.7993-1.8262	0.2384	367	0.2108	6644	7011	100
1.8262-1.8547	0.2206	317	0.2054	6668	6985	100
1.8547-1.8851	0.2264	329	0.1921	6702	7031	100
1.8851-1.9176	0.1916	337	0.1778	6659	6996	100
1.9176-1.9525	0.1906	383	0.1656	6655	7038	100
1.9525-1.99	0.1782	350	0.1606	6599	6949	100
1.99-2.0306	0.2018	351	0.157	6662	7013	100
2.0306-2.0748	0.1761	345	0.1572	6682	7027	100
2.0748-2.123	0.1841	334	0.1543	6655	6989	100
2.123-2.1761	0.1922	350	0.1507	6681	7031	100
2.1761-2.2349	0.1622	308	0.1431	6725	7033	100
2.2349-2.3007	0.1696	354	0.1446	6689	7043	100
2.3007-2.3749	0.162	375	0.1424	6629	7004	100
2.3749-2.4598	0.1909	344	0.1497	6647	6991	100
2.4598-2.5583	0.1699	339	0.1491	6710	7049	100
2.5583-2.6747	0.1722	360	0.154	6705	7065	100
2.6747-2.8156	0.1855	359	0.1564	6666	7025	100
2.8156-2.9919	0.1783	382	0.1488	6652	7034	100
2.9919-3.2228	0.1627	346	0.1366	6737	7083	100
3.2228-3.5469	0.1326	330	0.1222	6734	7064	100
3.5469-4.0595	0.1314	391	0.1145	6712	7103	100
4.0595-5.1121	0.1179	356	0.1039	6772	7128	100
5.1121-35.4382	0.1605	353	0.1482	6849	7202	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	0.5895	0.4533	-0.1442	1.0641	-0.1414	0.0593	0.1664	-0.0886	0.1269	0.35	-0.2626	0.0977	-0.2911	-0.2368	-0.3259	0.2882	0.0642	0.0427	0.2891	-0.1008	0.1582	-16.4375	26.1807	36.3804
2	0.5083	0.3529	-0.0306	0.7786	0.0418	0.0465	0.0009	-0.3454	-0.0039	0.3859	-0.2449	0.1365	-0.0268	-0.5046	-0.325	0.2161	0.0259	0.0746	0.3836	-0.1141	0.1958	-19.6502	17.3253	35.2061
3	0.885	-0.0064	0.1155	0.2942	0.3749	0.8181	0.0004	-0.3707	0.0188	0.1342	-0.0218	-0.0087	-0.12	0.2995	-0.0026	0.1503	-0.0704	-0.0415	0.2622	-0.001	0.1493	13.9873	16.9679	31.4334
4	0.3657	0.131	-0.1329	0.1543	0.1963	1.2601	0.0175	-0.0725	0.0721	0.0376	-0.0314	0.0173	-0.3503	-0.1349	-0.0813	0.1478	0.0336	-0.0018	0.073	-0.0098	0.1228	-7.5207	25.1323	12.0049
5	0.336	0.0045	-0.0551	0.315	0.0544	1.1943	0.0171	0.0083	-0.0846	-0.0063	-0.0152	0.0154	0.1387	-0.1798	-0.0049	0.0865	-0.0167	-0.0013	0.0714	-0.0036	0.1142	-8.3417	5.6856	3.2318
6	0.4986	0.0593	0.068	0.2813	0.0846	1.096	0.0149	-0.0866	-0.0293	0.0557	-0.0204	0.0182	0.0307	-0.1462	-0.0149	0.073	-0.0122	0.0018	0.0835	0.0032	0.1051	-8.137	9.515	13.1564
7	0.657	-0.055	0.2198	0.4014	-0.0873	0.1204	0.0277	0.1009	0.0122	-0.164	0.0112	-0.0326	-0.1053	0.2645	0.0571	0.1849	-0.054	0.0394	0.192	0.0347	0.1337	-17.7973	-5.7913	35.0928
8	0.3927	-0.0932	-0.107	0.3514	-0.0741	0.0725	-0.0594	0.167	-0.1684	-0.2463	0.0274	-0.2811	0.0182	0.3136	-0.0361	0.1713	-0.0248	0.0358	0.2126	0.0066	0.1847	-14.7261	-14.6925	36.3855
9	0.8039	0.0112	0.1618	0.3137	-0.2414	0.5197	-0.0218	0.4447	-0.052	-0.1503	0.0092	-0.0454	0.0115	-0.1402	0.0048	0.1599	0.0078	-0.0208	0.2519	-0.0231	0.1391	-46.6389	-19.1029	33.0819
10	0.4272	-0.0518	0.0025	0.2685	-0.0369	1.2611	0.0195	0.039	0.007	-0.0241	0.0021	-0.005	-0.1278	0.0804	0.0546	0.0754	-0.0053	0.0038	0.0151	-0.0039	0.0988	-30.2696	-13.1697	61.8977
11	0.4184	-0.0275	0.0388	0.186	-0.0405	0.9771	0.0083	0.0644	-0.0463	-0.0454	-0.0068	-0.0192	0.063	0.1353	-0.006	0.0893	0.0108	0.0005	0.0695	-0.0061	0.1254	-27.2461	-22.2594	58.2343

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 44 )	A	9 - 44
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 45 through 95 )	A	45 - 95
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 96 through 225 )	A	96 - 225
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 226 through 402 )	A	226 - 402
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 403 through 516 )	A	403 - 516
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 517 through 628 )	A	517 - 628
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 9 through 44 )	B	9 - 44
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 45 through 95 )	B	45 - 95
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 96 through 191 )	B	96 - 191
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 192 through 516 )	B	192 - 516
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 517 through 628 )	B	517 - 628

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