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- PDB-6jby: Crystal structure of endo-deglycosylated hydroxynitrile lyase iso... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jby | |||||||||
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Title | Crystal structure of endo-deglycosylated hydroxynitrile lyase isozyme 5 of Prunus communis | |||||||||
![]() | Hnl isoenzyme 5 | |||||||||
![]() | ![]() ![]() ![]() | |||||||||
Function / homology | ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zheng, Y.C. / Li, F.L. / Yu, H.L. / Xu, J.H. | |||||||||
![]() | ![]() Title: Structure-Guided Tuning of a Hydroxynitrile Lyase to Accept Rigid Pharmaco Aldehydes. Authors: Zheng, Y.C. / Li, F.L. / Lin, Z.M. / Lin, G.Q. / Hong, R. / Yu, H.L. / Xu, J.H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.7 KB | Display | ![]() |
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PDB format | ![]() | 100.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6lqyC ![]() 6lr8C ![]() 7bwpC ![]() 5eb4S 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
#1: Protein | Mass: 59186.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source | ||||
#3: Sugar | ChemComp-NAG / ![]() #4: Chemical | ChemComp-FAD / | ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.59 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Tris-bicine, calcium chloride, magnesium chloride, PEG 550MME, PEG 20000 PH range: 8.3-8.75 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.6→50 Å / Num. obs: 79762 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.031 / Rrim(I) all: 0.114 / Rsym value: 0.109 / Χ2: 0.993 / Net I/σ(I): 20.74 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 8.86 / Num. unique obs: 3877 / CC1/2: 0.973 / Rpim(I) all: 0.087 / Rrim(I) all: 0.321 / Rsym value: 0.309 / Χ2: 0.933 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5EB4 Resolution: 1.6→46.37 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 16.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→46.37 Å
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Refine LS restraints |
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LS refinement shell |
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