+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36635 | |||||||||
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Title | Structure of arginine oxidase from Pseudomonas sp. TRU 7192 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | OXIDOREDUCTASE | |||||||||
Biological species | Pseudomonas sp. (bacteria) | |||||||||
Method | 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 | 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36635.map.gz | 33.7 MB | EMDB map data format | |
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Header (meta data) | emd-36635-v30.xml emd-36635.xml | 17.5 KB 17.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36635_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_36635.png | 117.7 KB | ||
Masks | emd_36635_msk_1.map | 36.3 MB | Mask map | |
Filedesc metadata | emd-36635.cif.gz | 6.5 KB | ||
Others | emd_36635_half_map_1.map.gz emd_36635_half_map_2.map.gz | 28.9 MB 28.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36635 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36635 | HTTPS FTP |
-Validation report
Summary document | emd_36635_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_36635_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_36635_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | emd_36635_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36635 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36635 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_36635.map.gz / Format: CCP4 / Size: 36.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.96 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_36635_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36635_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36635_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : homooctamer of arginine oxidase
Entire | Name: homooctamer of arginine oxidase |
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Components |
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-Supramolecule #1: homooctamer of arginine oxidase
Supramolecule | Name: homooctamer of arginine oxidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Pseudomonas sp. (bacteria) / Strain: TPU 7192 |
Molecular weight | Theoretical: 540 KDa |
-Macromolecule #1: Amine oxidoreductase
Macromolecule | Name: Amine oxidoreductase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas sp. (bacteria) / Strain: TPU 7192 |
Molecular weight | Theoretical: 67.393164 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MHHHHHHMSQ TQPLDVAIIG GGVSGTYSAW RLQEAQGDHQ RIQLFEYSDR IGGRLFSINL PGLPNVVAEV GGMRWMPATK DNTGGHVMV DKLVGELKLE SKNFPMGSNL PDKDPVGAKD NLFYLRGERF RLRDFTEAPD KIPYKLAWSE RGYGPEDLQV K VMHNIYPG ...String: MHHHHHHMSQ TQPLDVAIIG GGVSGTYSAW RLQEAQGDHQ RIQLFEYSDR IGGRLFSINL PGLPNVVAEV GGMRWMPATK DNTGGHVMV DKLVGELKLE SKNFPMGSNL PDKDPVGAKD NLFYLRGERF RLRDFTEAPD KIPYKLAWSE RGYGPEDLQV K VMHNIYPG FDKLSLAEQM QVKVFGKEIW RYGFWDLLYR VLSNEGYQFM KDAGGYEANV ANASAVTQLP ATEYSDKTVF LA LKKGFQA LPLTLAKRFA EVPGGLIAGE QRIRMNRRLA SVQFSDDTEY PYRLHFQATR TVDGKTSDVP GAEEIIHARQ VIL ALPRRS LELIQSPLFD DPWLKENIDS VLVQSAFKLF LAYEQPWWRS QGLVAGRSVT DLPIRQCYYM GTECEQDGGE KTLN SLLMA SYNDIGTVPF WKGLEDGAPF EGYQPKSLQG RIDANEVVPK MQYQISEEMV RIAQRQVTSL HDQIELPAPY SAVYH AWDA DPFGGGWHEW KANYRLDLII QRMRHPVQEQ EVYIVGEAYS YGQGWVEGAL TTAESTLQDF FGLPRPAWLP EAYQLL PAP APVDIDNPPA LACTDCKKTL TEVTEFAYTG IKA |
-Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE
Macromolecule | Name: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 1 / Formula: FAD |
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Molecular weight | Theoretical: 785.55 Da |
Chemical component information | ChemComp-FAD: |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 29 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.5 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/2 / Material: MOLYBDENUM / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Instrument: LEICA KF80 |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 5035 / Average exposure time: 8.0 sec. / Average electron dose: 69.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 3.4 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Output model | PDB-8jt7: |