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- PDB-4gyl: The E142L mutant of the amidase from Geobacillus pallidus showing... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4gyl | ||||||
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Title | The E142L mutant of the amidase from Geobacillus pallidus showing the result of Michael addition of acrylamide at the active site cysteine | ||||||
![]() | Aliphatic amidase | ||||||
![]() | HYDROLASE / amidase / catalytic tetrad / amidase mechanism / acrylamide / Michael Adduct | ||||||
Function / homology | ![]() indoleacetamide hydrolase activity / amidase / beta-alanine biosynthetic process via 3-ureidopropionate / beta-ureidopropionase activity / amidase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Weber, B.W. / Sewell, B.T. / Kimani, S.W. / Varsani, A. / Cowan, D.A. / Hunter, R. | ||||||
![]() | ![]() Title: The mechanism of the amidases: mutating the glutamate adjacent to the catalytic triad inactivates the enzyme due to substrate mispositioning. Authors: Weber, B.W. / Kimani, S.W. / Varsani, A. / Cowan, D.A. / Hunter, R. / Venter, G.A. / Gumbart, J.C. / 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 | ![]() | 81.7 KB | Display | ![]() |
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PDB format | ![]() | 64.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 38624.875 Da / Num. of mol.: 1 / Mutation: E142L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ROP / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.68 % / Mosaicity: 0.226 ° |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1.2M sodium citrate, 0.4M sodium chloride, 0.1M sodium acetate, pH 5.6, vapor diffusion, hanging drop, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 22, 2011 / Details: VariMax HF Confocal Optical System | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: VariMax HF Confocal Optical System / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→24.23 Å / Num. obs: 30455 / % possible obs: 99.9 % / Redundancy: 15.98 % / Rmerge(I) obs: 0.246 / Χ2: 1.19 / Net I/σ(I): 7.8 / Scaling rejects: 3679 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.73 Å2 / Biso mean: 17.561 Å2 / Biso min: 10.24 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→24.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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