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- PDB-5nyc: A C145A mutant of Nesterenkonia AN1 amidase bound to propionitrile -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nyc | ||||||
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Title | A C145A mutant of Nesterenkonia AN1 amidase bound to propionitrile | ||||||
![]() | Amidase![]() | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kimani, S.W. / Sewell, B.T. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.1 KB | Display | ![]() |
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PDB format | ![]() | 50.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | 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 ( |
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Similar 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: 30068.686 Da / Num. of mol.: 1 / Mutation: C145A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Refinement | Method to determine structure![]() ![]() 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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