PDB-5zp3: Copper amine oxidase from Arthrobacter globiformis anaerobically ...

ID or keywords:

Entry

Database: PDB / ID: 5zp3

Title

Copper amine oxidase from Arthrobacter globiformis anaerobically reduced by ethylamine at pH 10 at 288 K (1)

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: 1.782 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_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_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 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5zp3.cif.gz	518.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5zp3.ent.gz	421.1 KB	Display	PDB format
PDBx/mmJSON format	5zp3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5zp3_validation.pdf.gz	462.9 KB	Display	wwPDB validaton report
Full document	5zp3_full_validation.pdf.gz	469.2 KB	Display
Data in XML	5zp3_validation.xml.gz	53.3 KB	Display
Data in CIF	5zp3_validation.cif.gz	79.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zp/5zp3 ftp://data.pdbj.org/pub/pdb/validation_reports/zp/5zp3	HTTPS FTP

-
Related structure data

Related structure data	5zouC 5zowC 5zoxC 5zoyC 5zozC 5zp0C 5zp1C 5zp2C 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	2cfg-d 5zpp-2 1iu7-d 5zou-d 5zpo-2 5zpi-d 5zoy-2 3x40-2 3x3x-2 3x40-1 2zl8-d 3x41-d 1wmp-d 5zpn-1 5zpt-1 5zps-1 1ivv-d 5zpb-d 5zpe-d 5zpq-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

-
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)	193.811, 64.969, 159.054
Angle α, β, γ (deg.)	90.000, 117.200, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-1248- HOH
2	1	B-1041- HOH
3	1	B-1186- HOH
4	1	B-1274- 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: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 932 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.23 Å³/Da / Density % sol: 61.93 %
Crystal grow	Temperature: 289 K / Method: microdialysis / pH: 7.4 / Details: 1.05M potassium-sodium tartrate, 25mM HEPES

-
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: 1.78→50 Å / Num. obs: 167742 / % possible obs: 99.9 % / Redundancy: 3.6 % / B_iso Wilson estimate: 20.94 Å² / R_merge(I) obs: 0.085 / R_pim(I) all: 0.051 / R_rim(I) all: 0.099 / Χ²: 3.743 / Net I/σ(I): 8.8 / Num. measured all: 610106

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
1.78-1.81	3.5	0.566	8319	0.793	0.353	0.669	1.077	99.5
1.81-1.84	3.5	0.486	8307	0.831	0.302	0.574	1.133	99.6
1.84-1.88	3.5	0.424	8289	0.866	0.264	0.501	1.145	99.7
1.88-1.92	3.5	0.34	8350	0.844	0.212	0.402	1.149	99.8
1.92-1.96	3.5	0.29	8396	0.932	0.179	0.341	1.21	99.9
1.96-2	3.6	0.245	8286	0.933	0.152	0.289	1.399	100
2-2.05	3.6	0.21	8338	0.962	0.129	0.247	1.396	100
2.05-2.11	3.6	0.194	8367	0.964	0.119	0.228	1.342	100
2.11-2.17	3.7	0.174	8412	0.962	0.106	0.204	1.583	100
2.17-2.24	3.7	0.154	8352	0.973	0.093	0.18	1.709	100
2.24-2.32	3.7	0.14	8351	0.975	0.084	0.164	1.798	100
2.32-2.42	3.7	0.133	8368	0.977	0.08	0.156	1.986	100
2.42-2.53	3.8	0.131	8340	0.978	0.078	0.152	2.305	100
2.53-2.66	3.8	0.128	8417	0.951	0.077	0.15	2.943	100
2.66-2.83	3.8	0.119	8445	0.975	0.071	0.139	3.882	100
2.83-3.04	3.8	0.109	8377	0.975	0.065	0.128	4.861	100
3.04-3.35	3.7	0.084	8413	0.985	0.05	0.098	5.477	100
3.35-3.83	3.7	0.057	8447	0.983	0.034	0.066	6.349	100
3.83-4.83	3.7	0.044	8510	0.991	0.027	0.052	9.941	100
4.83-50	3.5	0.05	8658	0.986	0.03	0.058	21.018	99.7

-
Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.11.1_2575	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: 1.782→33.274 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.75

	R_factor	Num. reflection	% reflection
R_free	0.1716	8355	4.99 %
R_work	0.1471	-	-
obs	0.1484	167564	99.62 %

Solvent computation

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

Displacement parameters

B_iso max: 184.19 Å² / B_iso mean: 27.7923 Å² / B_iso min: 8.91 Å²

Refinement step

Cycle: final / Resolution: 1.782→33.274 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9738	0	17	932	10687
B_iso mean	-	-	32	41.04	-
Num. residues	-	-	-	-	1240

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	10200
X-RAY DIFFRACTION	f_angle_d	0.852	13937
X-RAY DIFFRACTION	f_chiral_restr	0.061	1503
X-RAY DIFFRACTION	f_plane_restr	0.005	1858
X-RAY DIFFRACTION	f_dihedral_angle_d	6.909	8249

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 (%)
1.782-1.8023	0.2826	259	0.2563	5010	5269	94
1.8023-1.8235	0.2744	248	0.2413	5260	5508	100
1.8235-1.8457	0.2451	286	0.2249	5284	5570	100
1.8457-1.8691	0.246	288	0.2184	5268	5556	100
1.8691-1.8937	0.239	275	0.2033	5281	5556	100
1.8937-1.9196	0.2174	269	0.1906	5278	5547	100
1.9196-1.947	0.1962	263	0.1793	5271	5534	100
1.947-1.9761	0.2309	280	0.1731	5343	5623	100
1.9761-2.007	0.1992	252	0.1711	5302	5554	100
2.007-2.0399	0.1798	265	0.1644	5317	5582	100
2.0399-2.075	0.1938	296	0.1624	5280	5576	100
2.075-2.1128	0.1821	256	0.1545	5297	5553	100
2.1128-2.1534	0.185	275	0.1486	5303	5578	100
2.1534-2.1973	0.1786	273	0.1465	5303	5576	100
2.1973-2.2451	0.1737	277	0.1501	5350	5627	100
2.2451-2.2973	0.1833	268	0.153	5302	5570	100
2.2973-2.3548	0.1765	275	0.1487	5288	5563	100
2.3548-2.4184	0.193	316	0.1532	5313	5629	100
2.4184-2.4896	0.2019	272	0.1557	5362	5634	100
2.4896-2.5699	0.1973	292	0.1599	5262	5554	100
2.5699-2.6617	0.1962	290	0.1596	5324	5614	100
2.6617-2.7682	0.18	295	0.1549	5303	5598	100
2.7682-2.8941	0.1676	289	0.1514	5330	5619	100
2.8941-3.0466	0.1738	298	0.1495	5310	5608	100
3.0466-3.2374	0.1923	272	0.1432	5343	5615	100
3.2374-3.4871	0.1431	275	0.1246	5367	5642	100
3.4871-3.8375	0.131	304	0.1185	5332	5636	100
3.8375-4.3917	0.1287	269	0.1096	5383	5652	100
4.3917-5.529	0.1153	285	0.1101	5392	5677	100
5.529-33.2793	0.1786	293	0.1555	5451	5744	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	1.0202	-0.1518	-1.3556	4.8899	-0.66	2.5656	-0.0027	0.0062	0.0077	0.1855	-0.0917	0.2417	-0.2098	-0.3837	0.027	0.1627	0.0419	0.0294	0.2103	-0.0681	0.1683	175.8376	24.2051	34.9271
2	0.4153	0.0326	-0.1328	0.2883	0.0135	1.4314	0.006	-0.0753	0.0197	0.0466	-0.0157	-0.0132	-0.1395	0.0224	0.0157	0.1362	-0.0014	-0.0132	0.0939	-0.0015	0.1659	191.704	19.1459	16.684
3	0.6792	-0.0348	0.0729	0.278	0.0006	1.3347	-0.0165	-0.0251	-0.0133	0.0463	-0.0115	0.0188	0.0255	-0.1363	0.0257	0.1191	-0.0081	-0.0074	0.0962	-0.0076	0.1459	185.6447	11.5306	12.9162
4	1.2258	-0.0024	-1.3051	4.8252	0.2985	3.0989	0.011	-0.044	-0.0237	-0.1324	-0.0499	-0.273	-0.0609	0.369	-0.0298	0.1179	-0.0059	0.0502	0.1674	0.0483	0.17	177.4724	-7.4974	36.9387
5	7.0574	3.175	1.2054	1.6214	0.8998	1.416	-0.091	0.3872	0.3816	-0.0915	0.0249	-0.108	-0.0746	-0.0172	0.0709	0.2239	0.0278	0.0371	0.1643	0.0324	0.1202	167.7432	-14.2682	32.2709
6	1.097	0.0914	0.0876	0.3258	0.0478	1.2609	0.0005	0.2477	-0.0103	-0.0918	0.0205	0.0162	-0.1431	-0.0826	-0.018	0.1638	0.0328	-0.0111	0.1129	0.0264	0.1527	154.2629	-9.8912	46.9719
7	0.2579	-0.1532	-0.1837	0.2169	-0.0797	1.2665	0.0501	0.0375	0.0295	-0.0574	-0.0228	0.0142	-0.2778	-0.0084	-0.0067	0.1916	-0.0036	-0.0014	0.1248	-0.0056	0.1786	161.206	-5.9403	58.1848
8	0.4192	-0.0294	-0.0625	0.3746	-0.0149	1.1253	-0.0032	0.0111	-0.0467	-0.0124	-0.001	-0.0258	0.0972	0.1313	0.003	0.127	0.0131	-0.0079	0.1173	-0.0028	0.1718	165.9595	-22.4266	62.9765

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 72 )	A	9 - 72
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 73 through 516 )	A	73 - 516
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 517 through 628 )	A	517 - 628
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 9 through 72 )	B	9 - 72
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 73 through 114 )	B	73 - 114
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 115 through 277 )	B	115 - 277
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 278 through 402 )	B	278 - 402
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 403 through 628 )	B	403 - 628

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi