+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cyanide dihydratase from Bacillus pumilus C1 | |||||||||
![]() | Cyanide dihydratase from Bacillus pumilus C1 | |||||||||
![]() |
| |||||||||
![]() | Cyanide degrading enzyme / HYDROLASE | |||||||||
Function / homology | ![]() nitrilase activity / detoxification of nitrogen compound / nitrile hydratase activity Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.83 Å | |||||||||
![]() | Mulelu AE / Reitz J / van Rooyen JM / Scheffer M / Frangakis AS / Dlamini LS / Woodward JD / Benedik MJ / Sewell BT | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 7.9 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 11.8 KB 11.8 KB | Display Display | ![]() |
Images | ![]() | 47.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8p4iMC ![]() 8c5iC C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cyanide dihydratase from Bacillus pumilus C1 | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-
Sample components
-Entire : Wildtype cyanide dihydratase from Bacillus pumilus C1
Entire | Name: Wildtype cyanide dihydratase from Bacillus pumilus C1 |
---|---|
Components |
|
-Supramolecule #1: Wildtype cyanide dihydratase from Bacillus pumilus C1
Supramolecule | Name: Wildtype cyanide dihydratase from Bacillus pumilus C1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Homo-oligomeric 18mer expressed recombinantly without a purification tag. |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 0.666 kDa/nm |
-Macromolecule #1: Cyanide dihydratase
Macromolecule | Name: Cyanide dihydratase / type: protein_or_peptide / ID: 1 / Number of copies: 17 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 35.941418 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SIYPKFRAAA VQAAPIYLNL EASVEKSCEL IDEAASNGAK LVAFPEAFLP GYPWFAFIGH PEYTRKFYHE LYKNAVEIPS LAIQKISEA AKRNETYVCI SCSEKDGGSL YLAQLWFNPN GDLIGKHRKM RASVAERLIW GDGSGSMMPV FQTEIGNLGG L MCWEHQVP ...String: SIYPKFRAAA VQAAPIYLNL EASVEKSCEL IDEAASNGAK LVAFPEAFLP GYPWFAFIGH PEYTRKFYHE LYKNAVEIPS LAIQKISEA AKRNETYVCI SCSEKDGGSL YLAQLWFNPN GDLIGKHRKM RASVAERLIW GDGSGSMMPV FQTEIGNLGG L MCWEHQVP LDLMAMNAQN EQVHVASWPG YFDDEISSRY YAIATQTFVL MTSSIYTEEM KEMICLTQEQ RDYFETFKSG HT CIYGPDG EPISDMVPAE TEGIAYAEID VERVIDYKYY IDPAGHYSNQ SLSMNFNQQP TPVVKHLNHQ KNEVFTYEDI UniProtKB: Cyanide dihydratase |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | helical reconstruction |
Aggregation state | filament |
-
Sample preparation
Concentration | 0.2 mg/mL |
---|---|
Buffer | pH: 5.4 / Component - Concentration: 50.0 mM / Component - Formula: C6H8O7 / Component - Name: citrate |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK I |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 59.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 16.9 Å Applied symmetry - Helical parameters - Δ&Phi: -77 ° Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic) Resolution.type: BY AUTHOR / Resolution: 3.83 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 120943 |
---|---|
Startup model | Type of model: INSILICO MODEL |
Final angle assignment | Type: NOT APPLICABLE |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
---|---|
Output model | ![]() PDB-8p4i: |