+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1913 | |||||||||
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Title | Structure of the Listeria monocytogenes ClpP1P2 complex | |||||||||
Map data | This is a surface rendered side view of ClpP1P2 | |||||||||
Sample |
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Keywords | Proteomics / Vibralactone / heat shock protein / peptidase ClpP | |||||||||
Biological species | Listeria monocytogenes (bacteria) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 15.0 Å | |||||||||
Authors | Zeiler E / Braun N / Boettcher T / Kastenmueller A / Weinkauf S / Sieber S | |||||||||
Citation | Journal: Angew Chem Int Ed Engl / Year: 2011 Title: Vibralactone as a tool to study the activity and structure of the ClpP1P2 complex from Listeria monocytogenes. Authors: Evelyn Zeiler / Nathalie Braun / Thomas Böttcher / Andreas Kastenmüller / Sevil Weinkauf / Stephan A Sieber / | |||||||||
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_1913.map.gz | 2.7 MB | EMDB map data format | |
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Header (meta data) | emd-1913-v30.xml emd-1913.xml | 8.9 KB 8.9 KB | Display Display | EMDB header |
Images | 1913.jpg | 126.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1913 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1913 | HTTPS FTP |
-Validation report
Summary document | emd_1913_validation.pdf.gz | 202.7 KB | Display | EMDB validaton report |
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Full document | emd_1913_full_validation.pdf.gz | 201.8 KB | Display | |
Data in XML | emd_1913_validation.xml.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1913 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1913 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1913.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a surface rendered side view of ClpP1P2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.46 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Listeria monocytogenes ClpP1P2 complex
Entire | Name: Listeria monocytogenes ClpP1P2 complex |
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Components |
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-Supramolecule #1000: Listeria monocytogenes ClpP1P2 complex
Supramolecule | Name: Listeria monocytogenes ClpP1P2 complex / type: sample / ID: 1000 / Oligomeric state: Tetradecamer / Number unique components: 2 |
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Molecular weight | Experimental: 310 KDa / Theoretical: 310 KDa |
-Macromolecule #1: ClpP1
Macromolecule | Name: ClpP1 / type: protein_or_peptide / ID: 1 / Name.synonym: ClpP1 / Number of copies: 1 / Oligomeric state: Heptamer / Recombinant expression: Yes |
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Source (natural) | Organism: Listeria monocytogenes (bacteria) |
-Macromolecule #2: ClpP2
Macromolecule | Name: ClpP2 / type: protein_or_peptide / ID: 2 / Name.synonym: ClpP2 / Number of copies: 1 / Oligomeric state: Heptamer / Recombinant expression: Yes |
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Source (natural) | Organism: Listeria monocytogenes (bacteria) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7 / Details: 50 mM MES, 100 mM KCl, 5% glycerol |
Staining | Type: NEGATIVE Details: Grids with adsorbed protein floated on 1.5% w/v uranyl acetate for 30 seconds. |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | JEOL 100CX |
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Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification |
Image recording | Digitization - Scanner: OTHER / Number real images: 16 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Calibrated magnification: 58000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.8 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: eucentric / Specimen holder model: JEOL |
-Image processing
CTF correction | Details: Phase flipping |
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Final reconstruction | Applied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic / Number images used: 39116 |
Final two d classification | Number classes: 64 |