+Open data
-Basic information
Entry | Database: PDB / ID: 7dy0 | ||||||
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Title | 1.93 A cryo-EM structure of streptavidin | ||||||
Components | Streptavidin | ||||||
Keywords | CYTOSOLIC PROTEIN / STREPTAVIDIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.93 Å | ||||||
Authors | Hiraizumi, M. / Yamashita, K. / Nishizawa, T. / Kikkawa, M. / Nureki, O. | ||||||
Citation | Journal: To Be Published Title: 1.93 A cryo-EM structure of streptavidin Authors: Hiraizumi, M. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7dy0.cif.gz | 40.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dy0.ent.gz | 22.1 KB | Display | PDB format |
PDBx/mmJSON format | 7dy0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dy0_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7dy0_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7dy0_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 7dy0_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/7dy0 ftp://data.pdbj.org/pub/pdb/validation_reports/dy/7dy0 | HTTPS FTP |
-Related structure data
Related structure data | 30913MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10641 (Title: 1.93 A cryo-EM structure of streptavidin / Data size: 373.1 / Data #1: Unaligned movies [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: D2 (2x2 fold dihedral)) | ||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 18849.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629 |
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#2: Water | ChemComp-HOH / |
-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: Streptavidin / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Source (natural) | Organism: Streptomyces avidinii (bacteria) |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: coated grid with pentylamine before glow discharge / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 1.5 sec. / Electron dose: 70 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2277 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV |
-Processing
Software | Name: REFMAC / Version: 5.8.0272 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D2 (2x2 fold dihedral) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 1.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19045 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: RECIPROCAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5N7X Pdb chain-ID: M / Accession code: 5N7X / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 1.93→1.93 Å / Cor.coef. Fo:Fc: 0.814 / WRfactor Rwork: 0.349 / SU B: 6.443 / SU ML: 0.146 / Average fsc overall: 0.6654 / Average fsc work: 0.6654 / ESU R: 0.077 Details: Hydrogens have been added in their riding positions
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Solvent computation | Solvent model: BABINET MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.861 Å2
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Refine LS restraints |
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