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Yorodumi- EMDB-40671: Cryo-EM structure of Enoyl-CoA hydratase from Mycobacterium smegmatis -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40671 | |||||||||
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Title | Cryo-EM structure of Enoyl-CoA hydratase from Mycobacterium smegmatis | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase Ech1-like / enoyl-CoA hydratase / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / fatty acid beta-oxidation / ClpP/crotonase-like domain superfamily / lyase activity / Enoyl-CoA hydratase EchA21 Function and homology information | |||||||||
Biological species | Mycolicibacterium smegmatis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.85 Å | |||||||||
Authors | Shek R / Quispe J / Staker B / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of Enoyl-CoA hydratase from Mycobacterium smegmatis Authors: Shek R / Quispe J / Staker B / Phan IQ / Barrett LQ / Van Voorhis WC | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40671.map.gz | 9.5 MB | EMDB map data format | |
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Header (meta data) | emd-40671-v30.xml emd-40671.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40671_fsc.xml | 9.8 KB | Display | FSC data file |
Images | emd_40671.png | 33.6 KB | ||
Others | emd_40671_half_map_1.map.gz emd_40671_half_map_2.map.gz | 74.3 MB 74.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40671 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40671 | HTTPS FTP |
-Related structure data
Related structure data | 8soyMC 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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-Map
File | Download / File: emd_40671.map.gz / Format: CCP4 / Size: 80.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_40671_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40671_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Enoyl-CoA Hydratase hexamer
Entire | Name: Enoyl-CoA Hydratase hexamer |
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Components |
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-Supramolecule #1: Enoyl-CoA Hydratase hexamer
Supramolecule | Name: Enoyl-CoA Hydratase hexamer / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mycolicibacterium smegmatis (bacteria) |
-Macromolecule #1: Enoyl-CoA hydratase EchA21
Macromolecule | Name: Enoyl-CoA hydratase EchA21 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycolicibacterium smegmatis (bacteria) |
Molecular weight | Theoretical: 26.379848 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: YESVTVEVKD HVAQVTLIGP GKGNAMGPAF WEEMPDVFGT LDDDPDVRAI VLTGSGKNFS YGLDLPAMGA SLPALDAGAK SRSDFHKRL QKMQGAITAV ADCRTPTIAS VHGWCIGGGV DLISAVDIRY ASADAKFSVR EVKLAIVADV GSLARLPLIL S DGHLRELA ...String: YESVTVEVKD HVAQVTLIGP GKGNAMGPAF WEEMPDVFGT LDDDPDVRAI VLTGSGKNFS YGLDLPAMGA SLPALDAGAK SRSDFHKRL QKMQGAITAV ADCRTPTIAS VHGWCIGGGV DLISAVDIRY ASADAKFSVR EVKLAIVADV GSLARLPLIL S DGHLRELA LTGKDIDAAR AEKIGLVNDV YDDAEASLAA AHATAAEIAA NPPLTVAGVK DVLDAQRTAQ VAESLRYVAA WN SAFLPSK DLAEA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7 |
Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 296 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.6 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL |
Output model | PDB-8soy: |