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- EMDB-16437: Cyanide dihydratase from Bacillus pumilus C1 variant - Q86R,H305K... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Cyanide dihydratase from Bacillus pumilus C1 variant - Q86R,H305K,H308K,H323K | |||||||||
![]() | Map of cyanide dihydratase from Bacillus pumilus C1 variant (Q86R/H305K/H308K/H323K) | |||||||||
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![]() | Helical / homo-oligomeric / cyanide dihydratase / HYDROLASE | |||||||||
Function / homology | ![]() nitrilase activity / detoxification of nitrogen compound / nitrile hydratase activity Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.15 Å | |||||||||
![]() | Mulelu AE / Reitz J / van Rooyen J / Scheffer M / Frangakis AS / Dlamini LS / Woodward JD / Benedik MJ / Sewell BT | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The Role of Histidine Residues in the Oligomerization of Cyanide Dihydratase from Bacillus pumilus C1 Authors: Mulelu AE / Reitz J / van Rooyen J / Scheffer M / Frangakis AS / Dlamini LS / Woodward JD / Benedik MJ / Sewell BT | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 95.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13 KB 13 KB | Display Display | ![]() |
Images | ![]() | 39.3 KB | ||
Filedesc metadata | ![]() | 6.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 662.3 KB | Display | ![]() |
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Full document | ![]() | 661.9 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 7.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8c5iMC ![]() 8p4iC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Annotation | Map of cyanide dihydratase from Bacillus pumilus C1 variant (Q86R/H305K/H308K/H323K) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : Active helical nitrilase homo-oligomer of cyanide dihydratase fro...
Entire | Name: Active helical nitrilase homo-oligomer of cyanide dihydratase from Bacillus pumilus C1 variant (Q86R/H305K/H308K/H323K) |
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Components |
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-Supramolecule #1: Active helical nitrilase homo-oligomer of cyanide dihydratase fro...
Supramolecule | Name: Active helical nitrilase homo-oligomer of cyanide dihydratase from Bacillus pumilus C1 variant (Q86R/H305K/H308K/H323K) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Cyanide dihydratase from Bacillus pumilus C1 variant generated by site-directed mutagenesis. |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Cyanide dihydratase
Macromolecule | Name: Cyanide dihydratase / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 37.503363 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MTSIYPKFRA AAVQAAPIYL NLEASVEKSC ELIDEAASNG AKLVAFPEAF LPGYPWFAFI GHPEYTRKFY HELYKNAVEI PSLAIRKIS EAAKRNETYV CISCSEKDGG SLYLAQLWFN PNGDLIGKHR KMRASVAERL IWGDGSGSMM PVFQTEIGNL G GLMCWEHQ ...String: MTSIYPKFRA AAVQAAPIYL NLEASVEKSC ELIDEAASNG AKLVAFPEAF LPGYPWFAFI GHPEYTRKFY HELYKNAVEI PSLAIRKIS EAAKRNETYV CISCSEKDGG SLYLAQLWFN PNGDLIGKHR KMRASVAERL IWGDGSGSMM PVFQTEIGNL G GLMCWEHQ VPLDLMAMNA QNEQVHVASW PGYFDDEISS RYYAIATQTF VLMTSSIYTE EMKEMICLTQ EQRDYFETFK SG HTCIYGP DGEPISDMVP AETEGIAYAE IDVERVIDYK YYIDPAGHYS NQSLSMNFNQ QPTPVVKKLN KQKNEVFTYE DIQ YQKGIL EEKV UniProtKB: Cyanide dihydratase |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Concentration | 0.2 mg/mL | |||||||||
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Buffer | pH: 5.4 Component:
Details: 150 mM NaCl, 50 mM Tris-HCl pH 5.4 | |||||||||
Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 20.0 kPa | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: A 2.5 microlitre sample was applied onto a glow-discharged grid, blotted and plunged without incubation.. | |||||||||
Details | Homogeneous protein sample. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 54.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Number classes used: 92000 Applied symmetry - Helical parameters - Δz: 16.7 Å Applied symmetry - Helical parameters - Δ&Phi: -77 ° Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic) Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 103000 |
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Startup model | Type of model: INSILICO MODEL / In silico model: Featureless cylinder |
Final angle assignment | Type: NOT APPLICABLE |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-8c5i: |