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- PDB-8jm0: Endo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L331A f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8jm0 | ||||||
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Title | Endo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L331A from Prunus communis complexed with 2,2-dimethyl-4H-benzo[d][1,3]dioxine-6-carbaldehyde (Form A) | ||||||
![]() | (R)-mandelonitrile lyase | ||||||
![]() | LYASE / Hydroxynitrile lyase / FAD / hydrocynanation | ||||||
Function / homology | FLAVIN-ADENINE DINUCLEOTIDE / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zheng, Y.-C. / Li, F.-L. / Yu, H.-L. / Xu, J.-H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Endo-deglycosylated hydroxynitrile lyase isozyme 5 mutant from Prunus communis mutant L331A complexed with 2,2-dimethyl-4H-benzo[d][1,3]dioxine-6-carbaldehyde (Form A) Authors: Zheng, Y.-C. / Li, F.-L. / 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 | ![]() | 133.6 KB | Display | ![]() |
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PDB format | ![]() | 98.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 26.7 KB | Display | |
Data in CIF | ![]() | 39.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jm7C 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
-Protein , 1 types, 1 molecules A
#1: Protein | ( Mass: 58972.355 Da / Num. of mol.: 1 / Mutation: L331A Source method: isolated from a genetically manipulated source Details: Author stated the sequence reference is Genbank AAP84580.1, and the initial signal peptide (Met1 to Ser27) was exchanged into yeast alpha-factor subjected to cleavage during extracellular expression. Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 8 molecules ![](data/chem/img/NAG.gif)
#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 |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 416 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/BCN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/BCN.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-FQ3 / Mass: 192.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12O3 / Feature type: SUBJECT OF INVESTIGATION |
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#5: Chemical | ChemComp-FAD / |
#6: Chemical | ChemComp-PGE / |
#7: Chemical | ChemComp-PEG / |
#8: Chemical | ChemComp-BCN / |
#9: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.85 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: tris-bicine, 100 mM, pH 8.25; CaCl2, 60 mM; MgCl2, 60 mM; PEG 500MME, 24%, v/v; PEG 20000, 12%, w/v |
-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: Apr 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→50 Å / Num. obs: 56025 / % possible obs: 99.7 % / Redundancy: 12.1 % / CC1/2: 0.992 / CC star: 0.998 / Χ2: 0.938 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.79→1.83 Å / Redundancy: 11.6 % / Num. unique obs: 2744 / CC1/2: 0.727 / CC star: 0.918 / Χ2: 0.43 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 mean: 21.906 Å2
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Refinement step | Cycle: 1 / Resolution: 1.79→33.54 Å
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Refine LS restraints |
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