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Yorodumi- PDB-7cgs: Crystal endo-deglycosylated hydroxynitrile lyase isozyme 5 mutant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cgs | ||||||
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Title | Crystal endo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L343F from Prunus communis | ||||||
Components | (R)-mandelonitrile lyase | ||||||
Keywords | LYASE / Hydroxynitrile lyase / flavin protein | ||||||
Function / homology | Function and homology information mandelonitrile lyase activity / (R)-mandelonitrile lyase / oxidoreductase activity, acting on CH-OH group of donors / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Prunus dulcis (almond) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Zheng, Y.C. / Li, F.L. | ||||||
Citation | Journal: Chembiochem / Year: 2021 Title: A High-Throughput Screening Method for the Directed Evolution of Hydroxynitrile Lyase towards Cyanohydrin Synthesis. Authors: Zheng, Y.C. / Ding, L.Y. / Jia, Q. / Lin, Z. / Hong, R. / Yu, H.L. / Xu, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cgs.cif.gz | 140.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cgs.ent.gz | 102.6 KB | Display | PDB format |
PDBx/mmJSON format | 7cgs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/7cgs ftp://data.pdbj.org/pub/pdb/validation_reports/cg/7cgs | HTTPS FTP |
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-Related structure data
Related structure data | 6j8k S: Starting model for refinement |
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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
-Protein / Sugars , 2 types, 9 molecules A
#1: Protein | ( Mass: 59220.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Prunus dulcis (almond) / Gene: ALMOND_2B028509 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A5E4GBK6 |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 728 molecules
#2: Chemical | ChemComp-FAD / |
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#4: Chemical | ChemComp-TRS / |
#5: Chemical | ChemComp-BCN / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.09 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.25 Details: 100mM tris-bicine pH 8.5, 60mM CaCl2, 60mM MgCl2, 18% v/v PEG 500MME, 9% w/v PEG 20000 PH range: 8.25~8.75 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 77470 / % possible obs: 95.6 % / Redundancy: 12 % / CC1/2: 0.894 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.6→1.63 Å / Num. unique obs: 3723 / CC1/2: 0.89 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6J8K 6j8k Resolution: 1.6→46.52 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.401 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.075 / 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: 89.77 Å2 / Biso mean: 14.897 Å2 / Biso min: 7.08 Å2
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Refinement step | Cycle: final / Resolution: 1.6→46.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.602→1.643 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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