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Yorodumi- PDB-5nyc: A C145A mutant of Nesterenkonia AN1 amidase bound to propionitrile -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nyc | ||||||
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Title | A C145A mutant of Nesterenkonia AN1 amidase bound to propionitrile | ||||||
Components | Amidase | ||||||
Keywords | HYDROLASE / active site / amidase / nitrile / propionitrile / cysteine 145 / alanine 145 / nitrilase superfamily | ||||||
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 / Resolution: 1.51 Å | ||||||
Authors | Kimani, S.W. / Sewell, B.T. | ||||||
Funding support | South Africa, 1items
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Citation | Journal: To be published Title: Substrate recognition by an amidase of the nitrilase superfamily Authors: Kimani, S.W. / Venter, G.A. / 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 | 5nyc.cif.gz | 71.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nyc.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 5nyc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/5nyc ftp://data.pdbj.org/pub/pdb/validation_reports/ny/5nyc | HTTPS FTP |
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-Related structure data
Related structure data | 5nxzC 5ny2C 5ny7C 5nybC 5nyeC 5nz5C 3hkxS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 30068.686 Da / Num. of mol.: 1 / Mutation: C145A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nesterenkonia sp. 10004 (bacteria) / Gene: Nit2 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D0VWZ1, amidase | ||||
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#2: Chemical | #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: 47.93 % / Mosaicity: 0.52 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES sodium, 2% PEG 400, 2.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8856 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / 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: 1.51→28.43 Å / Num. all: 44728 / Num. obs: 44728 / % possible obs: 99.6 % / Redundancy: 7.4 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.073 / Rsym value: 0.067 / Net I/av σ(I): 7.2 / Net I/σ(I): 18.5 / Num. measured all: 331475 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HKX Resolution: 1.51→28.43 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.1651 / WRfactor Rwork: 0.138 / FOM work R set: 0.8976 / SU B: 0.97 / SU ML: 0.036 / SU R Cruickshank DPI: 0.057 / SU Rfree: 0.0602 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 58.32 Å2 / Biso mean: 15.138 Å2 / Biso min: 6.62 Å2
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Refinement step | Cycle: final / Resolution: 1.51→28.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.51→1.549 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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