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- PDB-7ycf: HYDROXYNITRILE LYASE FROM THE MILLIPEDE, Oxidus gracilis IN ACETO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ycf | ||||||||||||
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Title | HYDROXYNITRILE LYASE FROM THE MILLIPEDE, Oxidus gracilis IN ACETONITRILE | ||||||||||||
![]() | Hydroxynitrile lyase | ||||||||||||
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Function / homology | ![]() ![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Chaikaew, S. / Watanabe, Y. / Zheng, D. / Motojima, F. / Asano, Y. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-based site-directed mutagenesis of hydroxynitrile lyase from cyanogenic millipede, Oxidus gracilis for enhancing catalytic efficiency and enantioselectivity Authors: Chaikaew, S. / Watanabe, Y. / Zheng, D. / Motojima, F. / Asano, Y. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 266.6 KB | Display | ![]() |
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PDB format | ![]() | 211.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7yaxC ![]() 7ycbC ![]() 7ycdC ![]() 7yctC ![]() 6kfeS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 20383.896 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CNH / ![]() #3: Chemical | ChemComp-CL / ![]() #4: Chemical | ChemComp-SO4 / ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65.84 % |
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Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M BIS-TRIS containing 2.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Aug 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.01→61.56 Å / Num. obs: 73724 / % possible obs: 99.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.01→2.05 Å / Rmerge(I) obs: 0.302 / Num. unique obs: 4511 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6KFE Resolution: 2.01→53.365 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.164 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.117 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.328 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→53.365 Å
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Refine LS restraints |
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LS refinement shell |
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