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- PDB-7f8k: Room temperature structure of bacterial copper amine oxidase dete... -

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Basic information

Entry
Database: PDB / ID: 7f8k
TitleRoom temperature structure of bacterial copper amine oxidase determined by serial femtosecond crystallography
ComponentsPhenylethylamine oxidase
KeywordsOXIDOREDUCTASE / topaquinone copper serial femtosecond X-ray crystallography radiation-damage-free
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 / Phenylethylamine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MIR / Resolution: 2.2 Å
AuthorsMurakawa, T. / Okajima, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H05448 Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Microcrystal preparation for serial femtosecond X-ray crystallography of bacterial copper amine oxidase
Authors: Murakawa, T. / Suzuki, M. / Arima, T. / Sugahara, M. / Tanaka, T. / Tanaka, R. / Iwata, S. / Nango, E. / Tono, K. / Hayashi, H. / Fukui, K. / Yano, T. / Tanizawa, K. / Okajima, T.
History
DepositionJul 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8162
Polymers70,7531
Non-polymers641
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area27640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.750, 64.740, 93.550
Angle α, β, γ (deg.)90.000, 112.330, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-938-

HOH

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Components

#1: Protein Phenylethylamine oxidase / Primary amine oxidase / copper amine oxidase


Mass: 70752.742 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 289 K / Method: batch mode / pH: 7.4
Details: 1.05 M potassium-sodium tartrate in 25 mM HEPES buffer

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.771 Å
DetectorType: MPCCD / Detector: CCD / Date: Jun 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.771 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 87284 / % possible obs: 100 % / Redundancy: 147.3 % / Biso Wilson estimate: 49.62 Å2 / CC1/2: 0.9858935 / Net I/σ(I): 7.76
Reflection shellResolution: 2.2→2.278 Å / Num. unique obs: 8717 / CC1/2: 0.6180976

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Processing

Software
NameVersionClassification
PHENIXdev_3958refinement
CrystFELdata reduction
CrystFELdata scaling
PHASESphasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→19.96 Å / SU ML: 0.2447 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.1957
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1788 4374 5.01 %
Rwork0.1542 82910 -
obs0.1555 87284 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.79 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4868 0 1 175 5044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715019
X-RAY DIFFRACTIONf_angle_d0.88936843
X-RAY DIFFRACTIONf_chiral_restr0.0551740
X-RAY DIFFRACTIONf_plane_restr0.0094912
X-RAY DIFFRACTIONf_dihedral_angle_d6.3701696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.220.33551470.32762772X-RAY DIFFRACTION99.25
2.22-2.250.35261420.31022713X-RAY DIFFRACTION99.79
2.25-2.280.34571470.31212770X-RAY DIFFRACTION99.86
2.28-2.310.31361460.26512766X-RAY DIFFRACTION100
2.31-2.340.27021460.24232745X-RAY DIFFRACTION100
2.34-2.370.24271460.22682779X-RAY DIFFRACTION99.97
2.37-2.40.23341470.21652751X-RAY DIFFRACTION100
2.4-2.440.24951410.21622755X-RAY DIFFRACTION100
2.44-2.480.27371470.21712780X-RAY DIFFRACTION99.97
2.48-2.520.23331490.21462760X-RAY DIFFRACTION99.97
2.52-2.560.26381450.21542756X-RAY DIFFRACTION100
2.56-2.610.22411480.19922782X-RAY DIFFRACTION99.97
2.61-2.660.24491430.19192741X-RAY DIFFRACTION100
2.66-2.710.2141430.19322793X-RAY DIFFRACTION99.97
2.71-2.770.22981480.19252778X-RAY DIFFRACTION100
2.77-2.830.25311470.19582756X-RAY DIFFRACTION100
2.83-2.910.2571420.18562733X-RAY DIFFRACTION100
2.91-2.980.25371480.19022778X-RAY DIFFRACTION100
2.98-3.070.20591470.17992803X-RAY DIFFRACTION99.93
3.07-3.170.18781440.1752742X-RAY DIFFRACTION100
3.17-3.280.2081490.16522779X-RAY DIFFRACTION100
3.28-3.410.19111440.15872774X-RAY DIFFRACTION100
3.41-3.570.16531470.14282754X-RAY DIFFRACTION100
3.57-3.750.16081370.13582767X-RAY DIFFRACTION100
3.76-3.990.17821460.12762735X-RAY DIFFRACTION100
3.99-4.290.13071490.1222833X-RAY DIFFRACTION100
4.29-4.720.11761460.1062750X-RAY DIFFRACTION100
4.72-5.390.13461490.11092764X-RAY DIFFRACTION99.93
5.39-6.750.11691500.12742733X-RAY DIFFRACTION99.9
6.75-19.960.12881440.12522768X-RAY DIFFRACTION99.76

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