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- PDB-9fy7: Dye Type Peroxidase Aa from Streptomyces lividans with N3 ligand ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9fy7 | |||||||||
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Title | Dye Type Peroxidase Aa from Streptomyces lividans with N3 ligand by serial electron diffraction (SerialED) | |||||||||
![]() | Deferrochelatase | |||||||||
![]() | OXIDOREDUCTASE / serial electron diffraction / SerialED / DPtAa / oxireductase / heme | |||||||||
Function / homology | AZIDE ION / PROTOPORPHYRIN IX CONTAINING FE / : ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / ![]() | |||||||||
![]() | Hofer, G. / Wang, L. / Pacoste, L. / Hager, P. / Finjallaz, A. / Williams, L. / Worral, J. / Steiner, R. / Xu, H. / Zou, X. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Universal Serial electron diffraction for high quality protein structures Authors: Hofer, G. / Wang, L. / Pacoste, L. / Hager, P. / Fonjallaz, A. / Williams, L. / Worrall, J. / Steiner, R. / Xu, H. / Zou, X. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 292.4 KB | Display | ![]() |
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PDB format | ![]() | 234.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 627.1 KB | Display | ![]() |
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Full document | ![]() | 629.3 KB | Display | |
Data in XML | ![]() | 40 KB | Display | |
Data in CIF | ![]() | 59.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9fyhC ![]() 9fykC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 40039.824 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A7U8YY09, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: electron crystallography |
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Sample preparation
Component | Name: Dye type peroxidase Aa / Type: COMPLEX / Details: Dye type peroxidase Aa from Streptomyces lividans / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 81.75 kDa/nm / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7 |
Specimen | Conc.: 30 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Crystall slurry produced from dye type peroxidase Aa |
Specimen support | Grid material: COPPER / Grid type: C-flat-1/1 |
Vitrification | Cryogen name: ETHANE Details: Manual blotting in room temperature with ambient humidity |
-Data collection
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company | |||||||||||||||||||||
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Microscopy | Model: FEI TITAN KRIOS | |||||||||||||||||||||
Electron gun | Electron source: ![]() | |||||||||||||||||||||
Electron lens | Mode: DIFFRACTION / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm / Calibrated defocus min: 0 nm / Calibrated defocus max: 0 nm / Cs: 0 mm / C2 aperture diameter: 20 µm / Alignment procedure: BASIC | |||||||||||||||||||||
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 98 K / Temperature (min): 78 K | |||||||||||||||||||||
Image recording | Electron dose: 3.5 e/Å2 / Film or detector model: FEI CETA (4k x 4k) | |||||||||||||||||||||
EM diffraction shell |
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EM diffraction stats | Fourier space coverage: 79.62 % / High resolution: 1.1 Å / Num. of intensities measured: 250637 / Num. of structure factors: 220288 / Phase error: 35.84 ° / Phase error rejection criteria: 0 / Rmerge: 23 |
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Processing
EM software |
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Image processing | Details: FEI Ceta-D CMOS detector | ||||||||||||||||||||||||
EM 3D crystal entity | ∠α: 90 ° / ∠β: 105.8 ° / ∠γ: 90 ° / A: 72.77 Å / B: 67.4 Å / C: 73.63 Å / Space group name: P1211 / Space group num: 4 | ||||||||||||||||||||||||
CTF correction | Details: Diffraction experiment / Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 1.1 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL | ||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: RECIPROCAL | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 6I43 Accession code: 6I43 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell |
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