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- PDB-8jt7: Structure of arginine oxidase from Pseudomonas sp. TRU 7192 -

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Basic information

Entry
Database: PDB / ID: 8jt7
TitleStructure of arginine oxidase from Pseudomonas sp. TRU 7192
ComponentsAmine oxidoreductase
KeywordsOXIDOREDUCTASE
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesPseudomonas sp. (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.34 Å
AuthorsYamaguchi, H. / Numoto, N. / Suzuki, H. / Nishikawa, K. / Kamegawa, A. / Takahashi, K. / Sugiki, M. / Fujiyoshi, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis of arginine oxidase from Pseudomonas sp. TRU 7192
Authors: Yamaguchi, H. / Numoto, N. / Suzuki, H. / Nishikawa, K. / Kamegawa, A. / Takahashi, K. / Matsui, D. / Asano, Y. / Sugiki, M. / Fujiyoshi, Y.
History
DepositionJun 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amine oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1792
Polymers67,3931
Non-polymers7861
Water52229
1
A: Amine oxidoreductase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)545,43016
Polymers539,1458
Non-polymers6,2848
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation7
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
2generate(6.123234E-17, -1), (1, 6.123234E-17), (1)203.51997
3generate(-1, -1.2246468E-16), (1.2246468E-16, -1), (1)203.51997, 203.51997
4generate(-1.8369702E-16, 1), (-1, -1.8369702E-16), (1)1.42108547E-14, 203.51997
5generate(1), (-1, -1.2246468E-16), (1.2246468E-16, -1)203.51997, 203.51997
6generate(2.22044605E-16, 1, 8.65956056E-17), (1, 2.22044605E-16, -8.65956056E-17), (-8.65956056E-17, 8.65956056E-17, -1)-7.10542736E-14, -4.26325641E-14, 203.51997
7generate(2.22044605E-16, -1, 8.65956056E-17), (-1, 2.22044605E-16, 8.65956056E-17), (-8.65956056E-17, -8.65956056E-17, -1)203.51997, 203.51997, 203.51997
8generate(-1, 1.2246468E-16), (1), (-1.2246468E-16, -1)203.51997, 203.51997

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Components

#1: Protein Amine oxidoreductase


Mass: 67393.164 Da / Num. of mol.: 1 / Fragment: initiation methionine (1A), his-tags (2-7A)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: TPU 7192 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: homooctamer of arginine oxidase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.54 MDa / Experimental value: NO
Source (natural)Organism: Pseudomonas sp. (bacteria) / Strain: TPU 7192
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
250 mMsodium chlorideNaCl1
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: MOLYBDENUM / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA KF80 / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 3.4 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 8 sec. / Electron dose: 69.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5035
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2SerialEM3.8.9image acquisition
7Cootmodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
19REFMACmodel refinement
20Servalcat0.4.17model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D4 (2x4 fold dihedral)
3D reconstructionResolution: 2.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 254111 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model

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