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- PDB-9lz5: Reductive-half reaction intermediate of copper amine oxidase from... -

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Basic information

Entry
Database: PDB / ID: 9lz5
TitleReductive-half reaction intermediate of copper amine oxidase from Arthrobacter globiformis captured by mix-and-inject serial crystallography at 300-ms time delay
ComponentsPhenylethylamine oxidase
KeywordsOXIDOREDUCTASE / TPQ / topaquinone
Function / homology
Function and homology information


primary-amine oxidase / primary methylamine oxidase activity / amine metabolic process / quinone binding / copper ion binding
Similarity search - Function
: / AGAO-like N2 domain / : / 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 / 2-PHENYLETHYLAMINE / Phenylethylamine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsMurakawa, T. / Okajima, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22H04757 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Real-time capture of domain movements during copper amine oxidase catalysis by mix-and-inject serial crystallography.
Authors: Murakawa, T. / Suzuki, M. / Fukui, K. / Masuda, T. / Mizohata, E. / Miyahara, I. / Kurauchi, I. / Murakami, T. / Matsunaga, H. / Montawa, Y. / Nakajima, N. / Oozeki, T. / Sakai, K. / Son, T. ...Authors: Murakawa, T. / Suzuki, M. / Fukui, K. / Masuda, T. / Mizohata, E. / Miyahara, I. / Kurauchi, I. / Murakami, T. / Matsunaga, H. / Montawa, Y. / Nakajima, N. / Oozeki, T. / Sakai, K. / Son, T. / Higuchi, T. / Sunami, T. / Kimura, T. / Tono, K. / Tanaka, T. / Sugahara, M. / Arima, T. / Fangjia, L. / Kang, J. / Tanaka, R. / Iwata, S. / Nango, E. / Tosha, T. / Yano, T. / Tanizawa, K. / Okajima, T.
History
DepositionFeb 21, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release

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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)138,2458
Polymers137,8282
Non-polymers4176
Water15,439857
1
A: Phenylethylamine oxidase
hetero molecules

A: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,2458
Polymers137,8282
Non-polymers4176
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14830 Å2
ΔGint-77 kcal/mol
Surface area40620 Å2
MethodPISA
2
B: Phenylethylamine oxidase
hetero molecules

B: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,2458
Polymers137,8282
Non-polymers4176
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area14850 Å2
ΔGint-77 kcal/mol
Surface area40750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.832, 64.728, 158.520
Angle α, β, γ (deg.)90.000, 116.915, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11A-1121-

HOH

21A-1142-

HOH

31A-1187-

HOH

41B-1127-

HOH

51B-1144-

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: isolated from a natural source / Formula: Na
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-PEA / 2-PHENYLETHYLAMINE


Mass: 122.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12N / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 857 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.2 Å3/Da / Density % sol: 61.56 %
Crystal growTemperature: 289 K / Method: batch mode
Details: 1.05M potassium/sodium tartrate in 25mM HEPES buffer pH 7.4

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Data collection

DiffractionMean temperature: 299 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: Jan 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.87→30 Å / Num. obs: 282568 / % possible obs: 100 % / Redundancy: 84.8 % / CC1/2: 0.939793 / Net I/σ(I): 3.89
Reflection shellResolution: 1.87→1.97 Å / Num. unique obs: 28295 / CC1/2: 0.5214515
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
CrystFELdata scaling
PHASERphasing
CrystFELdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→29.82 Å / SU ML: 0.2553 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0429
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2126 14105 4.99 %
Rwork0.1879 268348 -
obs0.1891 282453 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.05 Å2
Refinement stepCycle: LAST / Resolution: 1.87→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9738 0 22 857 10617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005410342
X-RAY DIFFRACTIONf_angle_d0.829814158
X-RAY DIFFRACTIONf_chiral_restr0.05561530
X-RAY DIFFRACTIONf_plane_restr0.00791892
X-RAY DIFFRACTIONf_dihedral_angle_d6.27981486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.890.3844700.37948970X-RAY DIFFRACTION99.99
1.89-1.910.38224710.3569005X-RAY DIFFRACTION100
1.91-1.940.36154690.33338881X-RAY DIFFRACTION100
1.94-1.960.33854780.30649071X-RAY DIFFRACTION100
1.96-1.990.3224670.29178903X-RAY DIFFRACTION100
1.99-2.010.30324660.26948907X-RAY DIFFRACTION100
2.01-2.040.29354690.25968978X-RAY DIFFRACTION100
2.04-2.070.26854730.25219000X-RAY DIFFRACTION99.99
2.07-2.110.28054620.25398829X-RAY DIFFRACTION100
2.11-2.140.27974720.25129019X-RAY DIFFRACTION100
2.14-2.180.2634640.2498891X-RAY DIFFRACTION100
2.18-2.220.25814720.23018975X-RAY DIFFRACTION100
2.22-2.260.24054760.21338929X-RAY DIFFRACTION99.99
2.26-2.310.24644740.20538966X-RAY DIFFRACTION99.99
2.31-2.360.21254690.19858933X-RAY DIFFRACTION100
2.36-2.410.24244740.20279008X-RAY DIFFRACTION100
2.41-2.470.21884670.20168861X-RAY DIFFRACTION99.98
2.47-2.540.22124700.19728968X-RAY DIFFRACTION100
2.54-2.610.21844730.19838957X-RAY DIFFRACTION99.99
2.61-2.70.22014690.18528989X-RAY DIFFRACTION99.99
2.7-2.790.20184640.18418906X-RAY DIFFRACTION100
2.79-2.90.24054730.17768912X-RAY DIFFRACTION100
2.9-3.040.20384730.17478942X-RAY DIFFRACTION100
3.04-3.20.19624740.17028976X-RAY DIFFRACTION99.97
3.2-3.40.19484690.16068961X-RAY DIFFRACTION99.98
3.4-3.660.17044710.1488866X-RAY DIFFRACTION100
3.66-4.030.15244760.14498984X-RAY DIFFRACTION100
4.03-4.610.15384760.13258954X-RAY DIFFRACTION100
4.61-5.80.1694620.13978920X-RAY DIFFRACTION100
5.8-29.820.16894620.16348887X-RAY DIFFRACTION99.13

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