+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8077 | |||||||||
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Title | MicroED structure of proteinase K at 1.75 A resolution | |||||||||
Map data | None | |||||||||
Sample |
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Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | |||||||||
Biological species | Engyodontium album (fungus) | |||||||||
Method | electron crystallography / cryo EM / Resolution: 1.75 Å | |||||||||
Authors | Hattne J / Shi D | |||||||||
Citation | Journal: J Appl Crystallogr / Year: 2016 Title: Modeling truncated pixel values of faint reflections in MicroED images. Authors: Johan Hattne / Dan Shi / M Jason de la Cruz / Francis E Reyes / Tamir Gonen / Abstract: The weak pixel counts surrounding the Bragg spots in a diffraction image are important for establishing a model of the background underneath the peak and estimating the reliability of the integrated ...The weak pixel counts surrounding the Bragg spots in a diffraction image are important for establishing a model of the background underneath the peak and estimating the reliability of the integrated intensities. Under certain circumstances, particularly with equipment not optimized for low-intensity measurements, these pixel values may be corrupted by corrections applied to the raw image. This can lead to truncation of low pixel counts, resulting in anomalies in the integrated Bragg intensities, such as systematically higher signal-to-noise ratios. A correction for this effect can be approximated by a three-parameter lognormal distribution fitted to the weakly positive-valued pixels at similar scattering angles. The procedure is validated by the improved refinement of an atomic model against structure factor amplitudes derived from corrected micro-electron diffraction (MicroED) images. | |||||||||
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_8077.map.gz | 3 MB | EMDB map data format | |
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Header (meta data) | emd-8077-v30.xml emd-8077.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_8077.png | 206.5 KB | ||
Filedesc structureFactors | emd_8077_sf.cif.gz | 2.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8077 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8077 | HTTPS FTP |
-Validation report
Summary document | emd_8077_validation.pdf.gz | 636 KB | Display | EMDB validaton report |
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Full document | emd_8077_full_validation.pdf.gz | 635.6 KB | Display | |
Data in XML | emd_8077_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | emd_8077_validation.cif.gz | 4.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8077 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8077 | HTTPS FTP |
-Related structure data
Related structure data | 5i9sMC 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_8077.map.gz / Format: CCP4 / Size: 3.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.60105 Å / Y: 0.60105 Å / Z: 0.5739 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: Engyodontium album (fungus) |
Molecular weight | Theoretical: 28.98 KDa |
-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: Engyodontium album (fungus) |
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 UniProtKB: Proteinase K |
-Macromolecule #2: SULFATE ION
Macromolecule | Name: SULFATE ION / type: ligand / ID: 2 / Number of copies: 2 / 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: 133 / 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
Concentration | 25 mg/mL | ||||||
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Buffer | pH: 8 / Component:
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Number grids imaged: 1 / Number real images: 184 / Number diffraction images: 184 / Average exposure time: 4.1 sec. / Average electron dose: 0.004 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 1200 mm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |