+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41303 | |||||||||
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Title | Transmembrane map | |||||||||
Map data | Transmembrane map | |||||||||
Sample |
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Keywords | Peptidoglycan / glycosyltransferase / enzyme / MEMBRANE PROTEIN | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.97 Å | |||||||||
Authors | Nygaard R / Mancia F | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural basis of peptidoglycan synthesis by E. coli RodA-PBP2 complex Authors: Nygaard R / Graham CLB / Belcher Dufrisne M / Colburn JD / Pepe J / Hydorn MA / Corradi S / Brown CM / Ashraf KU / Vickery ON / Briggs NS / Deering JJ / Kloss B / Botta B / Clarke OB / ...Authors: Nygaard R / Graham CLB / Belcher Dufrisne M / Colburn JD / Pepe J / Hydorn MA / Corradi S / Brown CM / Ashraf KU / Vickery ON / Briggs NS / Deering JJ / Kloss B / Botta B / Clarke OB / Columbus L / Dworkin J / Stansfeld PJ / Roper DI / Mancia F | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41303.map.gz | 118.1 MB | EMDB map data format | |
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Header (meta data) | emd-41303-v30.xml emd-41303.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
Images | emd_41303.png | 118.4 KB | ||
Others | emd_41303_half_map_1.map.gz emd_41303_half_map_2.map.gz | 221.7 MB 221.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41303 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41303 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41303.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Transmembrane map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half Map 1
File | emd_41303_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 2
File | emd_41303_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : RodA-PBP2
Entire | Name: RodA-PBP2 |
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Components |
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-Supramolecule #1: RodA-PBP2
Supramolecule | Name: RodA-PBP2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Nanodisc were formed using MSP1E3D1 and POPG lipid |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 111.803 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.66 mg/mL | ||||||||||||
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Buffer | pH: 7 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 11120 / Average exposure time: 2.5 sec. / Average electron dose: 58.5 e/Å2 |
-Image processing
Particle selection | Number selected: 4415933 |
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Startup model | Type of model: OTHER |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12 and 3.2) / Software - details: Local refinement / Number images used: 399795 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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