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Basic information

Entry
Database: PDB / ID: 7ynh
TitleCatalytic intermediate of copper amine oxidase determined by serial femtosecond X-ray crystallography using a single-flow liquid jet system
ComponentsPhenylethylamine oxidase
KeywordsOXIDOREDUCTASE / topaquinone / copper amine oxidase / serial femtosecond X-ray crystallography
Function / homology
Function and homology information


: / : / : / primary-amine oxidase / 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 / PHENYLACETALDEHYDE / Phenylethylamine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsMurakawa, T. / Okajima, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H05448 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Serial femtosecond X-ray crystallography of an anaerobically formed catalytic intermediate of copper amine oxidase.
Authors: Murakawa, T. / Suzuki, M. / Fukui, K. / Masuda, T. / Sugahara, M. / Tono, K. / Tanaka, T. / Iwata, S. / Nango, E. / Yano, T. / Tanizawa, K. / Okajima, T.
History
DepositionJul 31, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenylethylamine oxidase
B: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,2418
Polymers137,8282
Non-polymers4136
Water16,069892
1
A: Phenylethylamine oxidase
hetero molecules

A: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,2418
Polymers137,8282
Non-polymers4136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14730 Å2
ΔGint-87 kcal/mol
Surface area40700 Å2
MethodPISA
2
B: Phenylethylamine oxidase
hetero molecules

B: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,2418
Polymers137,8282
Non-polymers4136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area14840 Å2
ΔGint-82 kcal/mol
Surface area40470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.510, 64.610, 158.240
Angle α, β, γ (deg.)90.000, 116.860, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1087-

HOH

21A-1164-

HOH

31B-1058-

HOH

41B-1159-

HOH

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Components

#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) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P46881, primary-amine oxidase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-HY1 / PHENYLACETALDEHYDE / Phenylacetaldehyde


Mass: 120.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 892 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.38 %
Crystal growTemperature: 289 K / Method: batch mode / pH: 7.4
Details: 1.05 M potassium/sodium tartrate in 25 mM HEPES buffer pH 7.4

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Data collection

DiffractionMean temperature: 299 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: Mar 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.94→30 Å / Num. obs: 251836 / % possible obs: 100 % / Redundancy: 49.6 % / CC1/2: 0.9224798 / Net I/σ(I): 3.11
Reflection shellResolution: 1.94→2.009 Å / Num. unique obs: 25243 / CC1/2: 0.5271663

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WA2

3wa2


Resolution: 1.94→29.76 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2095 12601 5.01 %
Rwork0.178 239131 -
obs0.1796 251732 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.68 Å2 / Biso mean: 31.2728 Å2 / Biso min: 12.56 Å2
Refinement stepCycle: final / Resolution: 1.94→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9738 0 22 892 10652
Biso mean--28.75 39.69 -
Num. residues----1240
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.94-1.960.30274210.283580648485100
1.96-1.990.30944210.278879368357100
1.99-2.010.29974170.275479838400100
2.01-2.030.28284220.260180168438100
2.03-2.060.31314210.257878668287100
2.06-2.090.28574260.252380138439100
2.09-2.120.27194220.250879578379100
2.12-2.150.2744180.242879648382100
2.15-2.180.25854170.237679608377100
2.18-2.220.2674250.228380408465100
2.22-2.260.25354180.213479008318100
2.26-2.30.25854220.215880248446100
2.3-2.340.23024170.206279598376100
2.34-2.390.23774170.210679628379100
2.39-2.440.2594210.209779808401100
2.44-2.50.24944190.207679298348100
2.5-2.560.24164180.201479578375100
2.56-2.630.22734230.187380178440100
2.63-2.710.22584220.180679678389100
2.71-2.80.2234170.181480148431100
2.8-2.90.1914210.172379778398100
2.9-3.010.21014240.172779098333100
3.01-3.150.23014210.166279818402100
3.15-3.320.18444150.15879788393100
3.32-3.520.17824230.142679998422100
3.52-3.790.16974200.136180268446100
3.8-4.180.1624230.130778998322100
4.18-4.780.13624200.125179808400100
4.78-6.010.15754180.139979828400100
6.01-29.760.1854120.16267892830499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.29790.3023-0.07880.6202-0.11780.03230.0451-0.18440.07440.3634-0.17520.1584-0.1713-0.3897-0.10360.33530.02860.03620.3513-0.08760.2313-17.883233.918634.7435
20.5488-0.1342-0.29740.0760.06830.4694-0.0104-0.4717-0.10520.1698-0.041-0.0214-0.00870.2651-0.01690.2597-0.0551-0.03040.40140.01840.24517.037124.428637.4442
30.38380.0469-0.05320.2394-0.02991.2560.0196-0.04020.01510.034-0.02070.0081-0.0913-0.08830.00060.14450.0064-0.00410.1302-0.00230.1824-6.03527.471410.0449
40.18820.0189-0.16780.1192-0.02980.13340.01840.0046-0.0014-0.1163-0.0515-0.09080.02470.1729-0.00940.2352-0.06310.01910.24050.02720.1971-16.23312.086136.669
50.47030.062-0.18910.0704-0.14970.5592-0.05230.3572-0.132-0.13270.0525-0.00550.0066-0.19890.00160.2088-0.0007-0.01020.2531-0.02230.2081-41.0811-7.466832.874
60.2642-0.0663-0.20980.21670.00141.14430.01020.0177-0.0074-0.02830.0211-0.0168-0.07140.11240.00480.1499-0.0065-0.00530.1243-0.00120.1958-29.2649-4.424760.7781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 72 )A9 - 72
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 191 )A73 - 191
3X-RAY DIFFRACTION3chain 'A' and (resid 192 through 628 )A192 - 628
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 72 )B9 - 72
5X-RAY DIFFRACTION5chain 'B' and (resid 73 through 191 )B73 - 191
6X-RAY DIFFRACTION6chain 'B' and (resid 192 through 628 )B192 - 628

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