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- PDB-4izw: The E41L mutant of the amidase from Nesterenkonia sp. AN1 showing... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4izw | ||||||
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Title | The E41L mutant of the amidase from Nesterenkonia sp. AN1 showing covalent addition of the acetamide moiety of fluoroacetamide at the active site cysteine | ||||||
![]() | Amidase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Kimani, S.W. / Sewell, B.T. | ||||||
![]() | ![]() Title: Covalent modifications of the active site cysteine occur as a result of mutating the glutamate of the catalytic triad in the amidase from Nesterenkonia sp. Authors: Kimani, S.W. / Hunter, R. / Vlok, M. / Watermeyer, J. / 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 | ![]() | 63.9 KB | Display | ![]() |
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PDB format | ![]() | 49.6 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: 30084.795 Da / Num. of mol.: 1 / Mutation: E41Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-ACM / ![]() | ||
#3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.16 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES sodium, 2% PEG 400, 2.0 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Detector: CCD / Date: Jul 10, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→42.87 Å / Num. obs: 35169 / % possible obs: 94 % / Redundancy: 2.61 % / Rmerge(I) obs: 0.076 / Χ2: 0.98 / Net I/σ(I): 7.9 / Scaling rejects: 695 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 31.3 / Model details: Phaser MODE: MR_AUTO
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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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.62 Å2 / Biso mean: 19.9973 Å2 / Biso min: 9.85 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→42.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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