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Yorodumi- PDB-4izv: The E41Q/C145A double mutant of the amidase from Nesterenkonia sp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4izv | ||||||
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Title | The E41Q/C145A double mutant of the amidase from Nesterenkonia sp. AN1 in complex with acrylamide | ||||||
Components | Amidase | ||||||
Keywords | hydrolase/substrate / hydrolase / active site / acrylamide (prop-2-enamide) / cysteine 145 / hydrolase-substrate complex | ||||||
Function / homology | Function and homology information amidase / indoleacetamide hydrolase activity / organonitrogen compound metabolic process / amidase activity Similarity search - Function | ||||||
Biological species | Nesterenkonia sp. 10004 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å | ||||||
Authors | Kimani, S.W. / Sewell, B.T. | ||||||
Citation | Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4izv.cif.gz | 65.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4izv.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 4izv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/4izv ftp://data.pdbj.org/pub/pdb/validation_reports/iz/4izv | HTTPS FTP |
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-Related structure data
-Links
-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: 30067.701 Da / Num. of mol.: 1 / Mutation: E41Q, C145A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nesterenkonia sp. 10004 (bacteria) / Strain: AN1 / Gene: Nit2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0VWZ1, amidase | ||
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#2: Chemical | ChemComp-ROP / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.95 % |
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Crystal grow | Temperature: 298 K Details: 2.0 M ammonium sulfate, vapor diffusion, sitting drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8856 |
Detector | Detector: CCD / Date: Nov 14, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→43.213 Å / Num. obs: 34247 / % possible obs: 98.9 % / Redundancy: 6.9 % / Rsym value: 0.074 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.389 / % possible all: 93.4 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 29.08 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→37.72 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.39 / SU B: 1.613 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0892 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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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 mean: 18.13 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→37.72 Å
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Refine LS restraints |
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