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- PDB-7wnp: Crystallographic structure of copper amine oxidase from Arthrobac... -

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Basic information

Entry
Database: PDB / ID: 7wnp
TitleCrystallographic structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4 determined by both X-ray and neutron diffraction data at 1.72 angstrom resolution.
ComponentsPhenylethylamine oxidase
KeywordsOXIDOREDUCTASE / 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
Copper amine oxidase copper-binding site signature. / Copper amine oxidase topaquinone signature. / Copper amine oxidase / Copper amine oxidase, catalytic domain / Copper amine oxidase, N-terminal / Copper amine oxidase, catalytic domain superfamily / Copper amine oxidase, enzyme domain
Similarity search - Domain/homology
COPPER (II) ION / DEUTERATED WATER / Phenylethylamine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.72 Å
AuthorsMurakawa, T. / Okajima, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP26440037 Japan
CitationJournal: Iucrj / Year: 2022
Title: Re-evaluation of protein neutron crystallography with and without X-ray/neutron joint refinement.
Authors: Murakawa, T. / Kurihara, K. / Adachi, M. / Kusaka, K. / Tanizawa, K. / Okajima, T.
History
DepositionJan 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0803
Polymers68,9941
Non-polymers872
Water17,294960
1
X: Phenylethylamine oxidase
hetero molecules

X: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,1616
Polymers137,9882
Non-polymers1734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area15170 Å2
ΔGint-98 kcal/mol
Surface area39720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.206, 61.979, 92.447
Angle α, β, γ (deg.)90.00, 112.06, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-1014-

DOD

21X-1188-

DOD

31X-1383-

DOD

41X-1518-

DOD

51X-1552-

DOD

61X-1661-

DOD

71X-1686-

DOD

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Components

#1: Protein Phenylethylamine oxidase / Primary amine oxidase


Mass: 68993.836 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 960 / Source method: isolated from a natural source / Formula: D2O
Has ligand of interestY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.33 %
Crystal growTemperature: 289 K / Method: microdialysis / pH: 7.4
Details: 1.05-M potassium sodium (Na) tartrate in 25-mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid buffer.

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SPALLATION SOURCEJPARC MLF BL-03J-PARC MLF BEAMLINE BL-0313.0-5.7
SYNCHROTRONPhoton Factory BL-5A21
Detector
TypeIDDetectorDate
iBIX1DIFFRACTOMETERNov 10, 2015
ADSC QUANTUM 315r2CCDMay 31, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
131
25.71
311
Reflection

Entry-ID: 7WNP

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rpim(I) allDiffraction-IDNet I/σ(I)CC starRsym value
1.72-20.947630687.42.66390.124914.99
1.72-5016138193.11.9125629.270.9950.053
Reflection shellResolution: 1.72→1.82 Å / Num. unique obs: 25457 / Rsym value: 0.233

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
Refinement

% reflection Rfree: 5 % / SU ML: 0.19 / Cross valid method: THROUGHOUT / Method to determine structure: MIR / Phase error: 19.57 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso max (Å2)Biso mean (Å2)Biso min (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection obs (%)Diffraction-IDσ(F)
1.72-32.06X-RAY DIFFRACTION100.7723.62346.940.18940.15510.15694296815688586497.1921.35
1.72-21NEUTRON DIFFRACTION0.23480.18880.191238097623786.5210
Refinement stepCycle: final / Resolution: 1.72→32.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4868 0 2 2860 7730
Biso mean--13.6 33.59 -
Num. residues----620
LS refinement shell

Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDNum. reflection allTotal num. of bins used% reflection obs (%)
1.72-1.740.3595750.31941407NEUTRON DIFFRACTION14822746
1.74-1.760.32231070.31362025NEUTRON DIFFRACTION21322766
1.76-1.790.31061130.312169NEUTRON DIFFRACTION22822771
1.79-1.810.37281220.2972315NEUTRON DIFFRACTION24372775
1.81-1.840.33111270.28332402NEUTRON DIFFRACTION25292778
1.84-1.870.31791260.2792396NEUTRON DIFFRACTION25222778
1.87-1.90.2921270.27182437NEUTRON DIFFRACTION25642780
1.9-1.930.34831340.26582553NEUTRON DIFFRACTION26872782
1.93-1.960.26811370.25782590NEUTRON DIFFRACTION27272784
1.96-20.29831390.24462637NEUTRON DIFFRACTION27762786
2-2.040.30681430.23242717NEUTRON DIFFRACTION28602789
2.04-2.090.28761460.22232760NEUTRON DIFFRACTION29062790
2.09-2.140.24961500.20322866NEUTRON DIFFRACTION30162792
2.14-2.190.23431500.20082880NEUTRON DIFFRACTION30302794
2.19-2.250.23671500.19732817NEUTRON DIFFRACTION29672791
2.25-2.320.24891470.18592846NEUTRON DIFFRACTION29932792
2.32-2.390.21691560.17372953NEUTRON DIFFRACTION31092795
2.39-2.480.27311550.16572969NEUTRON DIFFRACTION31242796
2.48-2.570.221580.16412987NEUTRON DIFFRACTION31452796
2.57-2.690.21581570.17052995NEUTRON DIFFRACTION31522797
2.69-2.830.24021600.17023052NEUTRON DIFFRACTION32122798
2.83-3.010.21221610.16953067NEUTRON DIFFRACTION32282798
3.01-3.240.20711600.16143045NEUTRON DIFFRACTION32052798
3.24-3.570.16981580.14012996NEUTRON DIFFRACTION31542796
3.57-4.080.17631570.12653002NEUTRON DIFFRACTION31592796
4.08-5.130.16141540.12672896NEUTRON DIFFRACTION30502792
5.13-210.20351400.16082649NEUTRON DIFFRACTION27892782
1.72-1.730.311130.24752138X-RAY DIFFRACTION22513078
1.73-1.760.28451430.23412735X-RAY DIFFRACTION28783099
1.76-1.780.27541450.21552749X-RAY DIFFRACTION28943098
1.78-1.80.29921460.21682772X-RAY DIFFRACTION29183099
1.8-1.820.26591440.21332719X-RAY DIFFRACTION28633098
1.82-1.850.23981460.19792758X-RAY DIFFRACTION290430100
1.85-1.870.21811440.18212761X-RAY DIFFRACTION29053099
1.87-1.90.22961440.17982713X-RAY DIFFRACTION28573099
1.9-1.930.24881450.1842781X-RAY DIFFRACTION29263098
1.93-1.960.21531440.1822725X-RAY DIFFRACTION28693098
1.96-20.21611440.18032751X-RAY DIFFRACTION28953099
2-2.030.23081440.17882727X-RAY DIFFRACTION28713099
2.03-2.070.22321440.18112757X-RAY DIFFRACTION29013098
2.07-2.120.20261460.17682735X-RAY DIFFRACTION28813099
2.12-2.160.20641440.16222737X-RAY DIFFRACTION28813098
2.16-2.210.17641460.15972779X-RAY DIFFRACTION29253099
2.21-2.270.18951450.15592749X-RAY DIFFRACTION28943099
2.27-2.330.18461440.15112727X-RAY DIFFRACTION28713098
2.33-2.40.17821450.15562775X-RAY DIFFRACTION29203099
2.4-2.470.22351470.15582801X-RAY DIFFRACTION29483099
2.47-2.560.20261470.15172763X-RAY DIFFRACTION29103099
2.56-2.660.2041450.16112780X-RAY DIFFRACTION29253099
2.66-2.790.19741470.15472769X-RAY DIFFRACTION29163099
2.79-2.930.20621460.15972772X-RAY DIFFRACTION29183099
2.93-3.120.18751440.15792750X-RAY DIFFRACTION28943098
3.12-3.360.17441430.1392723X-RAY DIFFRACTION28663097
3.36-3.690.13691440.11842721X-RAY DIFFRACTION28653096
3.69-4.230.13181410.11582696X-RAY DIFFRACTION28373095
4.23-5.320.15341420.11492669X-RAY DIFFRACTION28113094
5.32-32.060.1761340.17452536X-RAY DIFFRACTION26703087

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