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- PDB-9er3: Cyanide dihydratase from Bacillus pumilus C1 E155R variant with a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9er3 | ||||||
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Title | Cyanide dihydratase from Bacillus pumilus C1 E155R variant with altered helical twist. | ||||||
![]() | Cyanide dihydratase | ||||||
![]() | HYDROLASE / Left-handed helix. | ||||||
Function / homology | ![]() nitrilase activity / detoxification of nitrogen compound / nitrile hydratase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
![]() | Dlamini, L.S. / Woodward, J.D. / Sewell, B.T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cyanide dihydratase from Bacillus pumilus C1 E155R variant with altered helical twist Authors: Dlamini, L.S. / Woodward, J.D. / Sewell, B.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.1 MB | Display | ![]() |
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PDB format | ![]() | 1.8 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 158.4 KB | Display | |
Data in CIF | ![]() | 235.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 19910MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 36198.730 Da / Num. of mol.: 19 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Cyanide dihydratase from Bacillus pumilus C1 E155R variant with altered helical twist. Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.703 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 / Details: 50 mM NaCL, 50 mM Tris-HCl |
Buffer component | Conc.: 50 mM / Name: Tris-(hydroxymethyl) aminomethane / Formula: Tris-HCl |
Specimen | Conc.: 1.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.04 sec. / Electron dose: 1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 31418 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2387974 | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200866 / Algorithm: FOURIER SPACE / Num. of class averages: 50 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 101.248 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Details: The initial model was built ab initio using the map and amino acid sequence. Source name: Other / Type: other | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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