+Open data
-Basic information
Entry | Database: PDB / ID: 8jt7 | ||||||
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Title | Structure of arginine oxidase from Pseudomonas sp. TRU 7192 | ||||||
Components | Amine oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | FLAVIN-ADENINE DINUCLEOTIDE Function and homology information | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.34 Å | ||||||
Authors | Yamaguchi, H. / Numoto, N. / Suzuki, H. / Nishikawa, K. / Kamegawa, A. / Takahashi, K. / Sugiki, M. / Fujiyoshi, Y. | ||||||
Funding support | 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jt7.cif.gz | 128.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jt7.ent.gz | 98.4 KB | Display | PDB format |
PDBx/mmJSON format | 8jt7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jt7_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8jt7_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8jt7_validation.xml.gz | 31.9 KB | Display | |
Data in CIF | 8jt7_validation.cif.gz | 46.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/8jt7 ftp://data.pdbj.org/pub/pdb/validation_reports/jt/8jt7 | HTTPS FTP |
-Related structure data
Related structure data | 36635MC 8t8aC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | 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) |
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#2: Chemical | ChemComp-FAD / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: homooctamer of arginine oxidase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.54 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Pseudomonas sp. (bacteria) / Strain: TPU 7192 | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: MOLYBDENUM / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 | |||||||||||||||
Vitrification | Instrument: LEICA KF80 / Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: 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 holder | Cryogen: NITROGEN |
Image recording | Average 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 optics | Energyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D4 (2x4 fold dihedral) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 254111 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model |