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Yorodumi- PDB-7efd: 1.77 A cryo-EM structure of Streptavidin using first 40 frames (c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7efd | ||||||
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Title | 1.77 A cryo-EM structure of Streptavidin using first 40 frames (corresponding to about 40 e/A^2 total dose) | ||||||
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: 1.77 Å | ||||||
Authors | Hiraizumi, M. / Yamashita, K. / Nishizawa, T. / Kotecha, A. / Nureki, O. | ||||||
Citation | Journal: To Be Published Title: 1.77 A cryo-EM structure of Streptavidin using first 40 frames (corresponding to about 40e/A^2 total dose) 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 | 7efd.cif.gz | 42.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7efd.ent.gz | 24.5 KB | Display | PDB format |
PDBx/mmJSON format | 7efd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7efd_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7efd_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7efd_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 7efd_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/7efd ftp://data.pdbj.org/pub/pdb/validation_reports/ef/7efd | HTTPS FTP |
-Related structure data
Related structure data | 31084MC 7efcC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-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: Chemical | ChemComp-BTN / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-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 | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | 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 | Electron dose: 70 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4053 |
-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: 1.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153976 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: RECIPROCAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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Refinement | Resolution: 1.77→76.255 Å / Cor.coef. Fo:Fc: 0.895 / WRfactor Rwork: 0.349 / SU B: 3.828 / SU ML: 0.099 / Average fsc overall: 0.6978 / Average fsc work: 0.6978 / ESU R: 0.053 Details: Hydrogens have been added in their riding positions
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Solvent computation | Solvent model: BABINET MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.492 Å2
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