PDB-7wir: Holo form of N381A mutant of copper amine oxidase from Arthrobact...

ID or keywords:

Entry

Database: PDB / ID: 7wir

Title

Holo form of N381A mutant of copper amine oxidase from Arthrobacter globiformis

Components

Phenylethylamine oxidase

Keywords

OXIDOREDUCTASE / topaquinone / TPQ / amine oxidase

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: 1.5 Å

Authors

Murakawa, T. / Okajima, T.

Funding support

Japan, 1items

Citation

Journal: Chem Sci / Year: 2022
Title: Molecular mechanism of a large conformational change of the quinone cofactor in the semiquinone intermediate of bacterial copper amine oxidase.
Authors: Shoji, M. / Murakawa, T. / Nakanishi, S. / Boero, M. / Shigeta, Y. / Hayashi, H. / Okajima, T.

History

Deposition	Jan 4, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 16, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7wir.cif.gz	526.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7wir.ent.gz	430.5 KB	Display	PDB format
PDBx/mmJSON format	7wir.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7wir_validation.pdf.gz	482.3 KB	Display	wwPDB validaton report
Full document	7wir_full_validation.pdf.gz	507.7 KB	Display
Data in XML	7wir_validation.xml.gz	65.7 KB	Display
Data in CIF	7wir_validation.cif.gz	100 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wi/7wir ftp://data.pdbj.org/pub/pdb/validation_reports/wi/7wir	HTTPS FTP

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Related structure data

Related structure data	7wisC 1iu7S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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

141 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	192.967, 63.016, 158.013
Angle α, β, γ (deg.)	90.00, 117.63, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-1034- HOH
2	1	B-925- HOH

#1: Protein	Phenylethylamine oxidase / Primary amine oxidase / Copper amine oxidase Mass: 68869.695 Da / Num. of mol.: 2 / Mutation: N381A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Production host: Escherichia coli (E. coli) / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1539 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 3.09 Å³/Da / Density % sol: 60.19 %
Crystal grow	Temperature: 289 K / Method: microdialysis / pH: 6.8 / Details: 25 mM HEPES 1.05 M potassium sodium tartrate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SPring-8

/ Beamline: BL44XU / Wavelength: 0.9 Å

Detector

Type: Bruker DIP-6040 / Detector: IMAGE PLATE / Date: Jul 1, 2007

Radiation

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

Radiation wavelength

Wavelength: 0.9 Å / Relative weight: 1

Reflection

Resolution: 1.5→139.991 Å / Num. all: 265999 / Num. obs: 265999 / % possible obs: 99 % / Redundancy: 3.6 % / B_iso Wilson estimate: 15.28 Å² / R_pim(I) all: 0.056 / R_rim(I) all: 0.107 / R_sym value: 0.091 / Net I/av σ(I): 2.8 / Net I/σ(I): 8.7 / Num. measured all: 964630

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique obs	R_pim(I) all	R_rim(I) all	R_sym value	Net I/σ(I) obs	% possible all
1.5-1.58	3.5	0.473	1.4	133818	37966	0.288	0.554	0.473	2.5	97.1
1.58-1.68	3.5	0.331	2.1	128418	36290	0.202	0.388	0.331	3.5	98.3
1.68-1.79	3.6	0.232	2.8	123197	34465	0.141	0.272	0.232	4.8	98.9
1.79-1.94	3.6	0.157	3.6	116124	32109	0.095	0.183	0.157	7	99.2
1.94-2.12	3.7	0.114	4.2	108562	29672	0.069	0.133	0.114	9.8	99.4
2.12-2.37	3.7	0.095	4.7	100487	27039	0.057	0.111	0.095	12.2	99.9
2.37-2.74	3.8	0.085	4.7	89710	23914	0.051	0.099	0.085	14.1	100
2.74-3.35	3.8	0.077	4.8	75981	20219	0.047	0.09	0.077	16.4	100
3.35-4.74	3.7	0.073	5.4	58009	15721	0.046	0.087	0.073	17.6	99.9
4.74-22.451	3.5	0.072	5.4	30324	8604	0.047	0.086	0.072	16.6	97.8

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
SCALA	3.3.22	data scaling
PDB_EXTRACT	3.27	data extraction
MOSFLM		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1IU7

1iu7

Resolution: 1.5→22.45 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 18.72 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.181	13214	4.97 %
R_work	0.161	-	-
obs	0.162	265921	99 %

Solvent computation

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

Displacement parameters

B_iso mean: 23.37 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→22.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9732	0	182	1540	11454

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	10451
X-RAY DIFFRACTION	f_angle_d	1.504	14243
X-RAY DIFFRACTION	f_dihedral_angle_d	14.99	3878
X-RAY DIFFRACTION	f_chiral_restr	0.105	1522
X-RAY DIFFRACTION	f_plane_restr	0.022	1880

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 (%)
1.5-1.517	0.3176	442	0.3059	8179	X-RAY DIFFRACTION	97
1.517-1.5349	0.3077	456	0.3	8219	X-RAY DIFFRACTION	97
1.5349-1.5536	0.2644	429	0.273	8088	X-RAY DIFFRACTION	97
1.5536-1.5733	0.2913	482	0.2641	8282	X-RAY DIFFRACTION	98
1.5733-1.5939	0.2585	447	0.2518	8246	X-RAY DIFFRACTION	97
1.5939-1.6158	0.2665	411	0.2414	8396	X-RAY DIFFRACTION	98
1.6158-1.6389	0.2457	423	0.2236	8254	X-RAY DIFFRACTION	98
1.6389-1.6633	0.2357	471	0.2133	8395	X-RAY DIFFRACTION	99
1.6633-1.6893	0.2236	401	0.2067	8339	X-RAY DIFFRACTION	99
1.6893-1.717	0.2246	431	0.194	8379	X-RAY DIFFRACTION	99
1.717-1.7466	0.2176	405	0.1908	8426	X-RAY DIFFRACTION	99
1.7466-1.7783	0.1935	427	0.1799	8416	X-RAY DIFFRACTION	99
1.7783-1.8125	0.2114	450	0.1764	8409	X-RAY DIFFRACTION	99
1.8125-1.8495	0.1953	435	0.1711	8434	X-RAY DIFFRACTION	99
1.8495-1.8897	0.179	470	0.161	8362	X-RAY DIFFRACTION	99
1.8897-1.9336	0.174	415	0.1542	8444	X-RAY DIFFRACTION	99
1.9336-1.9819	0.1692	472	0.1521	8428	X-RAY DIFFRACTION	99
1.9819-2.0355	0.1759	441	0.1475	8434	X-RAY DIFFRACTION	99
2.0355-2.0954	0.1718	432	0.1475	8481	X-RAY DIFFRACTION	99
2.0954-2.1629	0.1699	426	0.1464	8493	X-RAY DIFFRACTION	100
2.1629-2.2402	0.1715	460	0.1465	8497	X-RAY DIFFRACTION	100
2.2402-2.3298	0.1677	423	0.1436	8530	X-RAY DIFFRACTION	100
2.3298-2.4357	0.1691	455	0.1455	8515	X-RAY DIFFRACTION	100
2.4357-2.5639	0.1812	471	0.152	8471	X-RAY DIFFRACTION	100
2.5639-2.7243	0.181	475	0.1511	8526	X-RAY DIFFRACTION	100
2.7243-2.9342	0.1742	441	0.1508	8553	X-RAY DIFFRACTION	100
2.9342-3.2288	0.1603	450	0.1433	8576	X-RAY DIFFRACTION	100
3.2288-3.6942	0.1456	412	0.1339	8618	X-RAY DIFFRACTION	100
3.6942-4.6475	0.1445	418	0.1286	8655	X-RAY DIFFRACTION	100
4.6475-22.4531	0.174	443	0.1655	8662	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	0.7754	-0.1384	-0.0082	0.813	0.1576	0.0983	0.0734	0.2683	-0.0839	-0.4005	-0.1206	-0.172	-0.103	0.2808	-0.0987	0.2681	-0.0397	0.0671	0.439	0.1111	0.18	48.9752	4.9916	0.6514
2	0.7278	-0.0768	0.1026	0.3246	-0.2625	0.6982	0.0173	0.4596	-0.0461	-0.1961	-0.0634	-0.0248	-0.0715	-0.0674	-0.0814	0.1751	0.0517	-0.0225	0.3043	-0.0058	0.147	21.4978	-0.4043	2.5589
3	0.3158	-0.1831	-0.1427	0.243	-0.1445	0.7932	0.0119	0.1315	0.064	-0.0796	-0.0377	-0.0412	-0.2755	0.1813	-0.1127	0.1555	-0.0407	0.0057	0.1429	0.0346	0.1311	38.6871	8.6156	22.7858
4	0.4904	-0.1368	0.0939	0.302	-0.025	1.1382	0.0263	0.1131	-0.0421	-0.0277	-0.0293	-0.0181	0.0866	0.2116	0.01	0.0836	0.0208	0.0033	0.1106	0.0021	0.105	37.923	-9.021	27.3071
5	0.618	-0.1429	-0.0416	0.2253	0.2109	0.3205	0.0008	-0.0539	-0.0263	0.0568	-0.014	0.0705	-0.0278	-0.1787	0.0016	0.1378	0.0514	0.0022	0.1624	-0.0427	0.1323	11.0462	7.5861	68.8326
6	0.4973	-0.0105	0.0685	0.1765	0.137	0.7931	-0.0521	-0.1685	0.013	0.0697	0.0343	0.0082	-0.0471	0.1474	-0.0078	0.1477	-0.0069	-0.0308	0.1335	-0.0043	0.1595	38.025	1.1056	67.2815
7	0.3918	0.0572	-0.1365	0.0708	0.2942	0.7667	-0.0087	-0.0355	0.0548	0.0093	-0.003	0.0242	-0.2617	-0.0952	-0.0556	0.1572	0.0312	-0.0045	0.0603	0.0019	0.124	21.7971	9.6813	46.8707
8	0.4636	0.0064	0.1366	0.2471	0.0835	1.0296	0.0043	-0.0198	-0.0434	0.014	-0.0061	0.0133	0.0563	-0.1074	-0.0174	0.0758	-0.001	0.0036	0.0477	0.0045	0.1003	21.6602	-7.9285	43.0635

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 225 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 226 THROUGH 402 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 403 THROUGH 628 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 9 THROUGH 72 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 73 THROUGH 225 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 226 THROUGH 402 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 403 THROUGH 628 )

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