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Yorodumi- EMDB-0865: MicroED structure of proteinase K at 1.50A determained using crys... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0865 | |||||||||||||||
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Title | MicroED structure of proteinase K at 1.50A determained using crystal lamellas prepared by focused ion beam milling | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Function / homology | Function and homology information peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Parengyodontium album (fungus) / Tritirachium album,Engyodontium album | |||||||||||||||
Method | electron crystallography / cryo EM / Resolution: 1.5 Å | |||||||||||||||
Authors | Zhou H / Luo Z / Li X | |||||||||||||||
Funding support | China, 4 items
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Citation | Journal: J Struct Biol / Year: 2019 Title: Using focus ion beam to prepare crystal lamella for electron diffraction. Authors: Heng Zhou / Zhipu Luo / Xueming Li / Abstract: Electron diffraction provides a powerful tool to solve the structures of small protein crystals. However, strong interactions between the electrons and the materials limit the application of the ...Electron diffraction provides a powerful tool to solve the structures of small protein crystals. However, strong interactions between the electrons and the materials limit the application of the electron crystallographic method on large protein crystals with micrometer or larger sizes. Here, we used the focused ion beam (FIB) equipped on the scanning electron microscope (SEM) to mill a large crystal to thin lamella. The influences of the milling on the crystal lamella were observed and investigated, including radiation damage on the crystal surface during the FIB imaging, deformation of the thin crystal lamella, and variation in the diffraction intensities under electron radiation. These observations provide important information to optimize the FIB milling, and hence is important to obtain high-quality crystal samples for routine structure determination of protein crystals using the electron cryo-microscope. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0865.map.gz | 5.4 MB | EMDB map data format | |
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Header (meta data) | emd-0865-v30.xml emd-0865.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | emd_0865.png | 202.3 KB | ||
Filedesc structureFactors | emd_0865_sf.cif.gz | 992.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0865 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0865 | HTTPS FTP |
-Validation report
Summary document | emd_0865_validation.pdf.gz | 512.7 KB | Display | EMDB validaton report |
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Full document | emd_0865_full_validation.pdf.gz | 512.2 KB | Display | |
Data in XML | emd_0865_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | emd_0865_validation.cif.gz | 4.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0865 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0865 | HTTPS FTP |
-Related structure data
Related structure data | 6lawMC 0864C 6lavC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0865.map.gz / Format: CCP4 / Size: 5.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X: 0.4951 Å / Y: 0.4951 Å / Z: 0.50056 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 96 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : proteinase K
Entire | Name: proteinase K |
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Components |
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-Supramolecule #1: proteinase K
Supramolecule | Name: proteinase K / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Parengyodontium album (fungus) |
-Macromolecule #1: Proteinase K
Macromolecule | Name: Proteinase K / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidase K |
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Source (natural) | Organism: Tritirachium album,Engyodontium album |
Molecular weight | Theoretical: 28.958791 KDa |
Sequence | String: AAQTNAPWGL ARISSTSPGT STYYYDESAG QGSCVYVIDT GIEASHPEFE GRAQMVKTYY YSSRDGNGHG THCAGTVGSR TYGVAKKTQ LFGVKVLDDN GSGQYSTIIA GMDFVASDKN NRNCPKGVVA SLSLGGGYSS SVNSAAARLQ SSGVMVAVAA G NNNADARN ...String: AAQTNAPWGL ARISSTSPGT STYYYDESAG QGSCVYVIDT GIEASHPEFE GRAQMVKTYY YSSRDGNGHG THCAGTVGSR TYGVAKKTQ LFGVKVLDDN GSGQYSTIIA GMDFVASDKN NRNCPKGVVA SLSLGGGYSS SVNSAAARLQ SSGVMVAVAA G NNNADARN YSPASEPSVC TVGASDRYDR RSSFSNYGSV LDIFGPGTDI LSTWIGGSTR SISGTSMATP HVAGLAAYLM TL GKTTAAS ACRYIADTAN KGDLSNIPFG TVNLLAYNNY QA |
-Macromolecule #2: SULFATE ION
Macromolecule | Name: SULFATE ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: SO4 |
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Molecular weight | Theoretical: 96.063 Da |
Chemical component information | ChemComp-SO4: |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 230 / 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 | electron crystallography |
Aggregation state | 3D array |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 0.028 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 1000 mm |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 1.5 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES |
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Crystal parameters | Unit cell - A: 69.31 Å / Unit cell - B: 69.31 Å / Unit cell - C: 104.12 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Space group: P 43 21 2 |
Crystallography statistics | Number intensities measured: 200471 / Number structure factors: 37742 / Fourier space coverage: 91.1 / R sym: 0.245 / R merge: 0.245 / Overall phase error: 0 / Overall phase residual: 1 / Phase error rejection criteria: 60 / High resolution: 1.5 Å / Shell - Shell ID: 1 / Shell - High resolution: 1.5 Å / Shell - Low resolution: 1.55 Å / Shell - Number structure factors: 3693 / Shell - Phase residual: 1 / Shell - Fourier space coverage: 90.6 / Shell - Multiplicity: 5.2 |
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-6law: |