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Yorodumi- PDB-6lqy: Crystal complex of endo-deglycosylated hydroxynitrile lyase isozy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lqy | ||||||
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Title | Crystal complex of endo-deglycosylated hydroxynitrile lyase isozyme 5 of Prunus communis with benzaldehyde | ||||||
Components | PREDICTED: (R)-mandelonitrile lyase | ||||||
Keywords | LYASE / Endo-deglycosylated / GMC oxidoreductases N and C superfamily / Flavoprotein | ||||||
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 / Resolution: 1.598 Å | ||||||
Authors | Zheng, Y.C. / Li, F.L. / Yu, H.L. / Xu, J.H. | ||||||
Citation | Journal: Acs Catalysis / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lqy.cif.gz | 135.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lqy.ent.gz | 98.8 KB | Display | PDB format |
PDBx/mmJSON format | 6lqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/6lqy ftp://data.pdbj.org/pub/pdb/validation_reports/lq/6lqy | HTTPS FTP |
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-Related structure data
Related structure data | 6jbyC 6lr8C 7bwpC 5eb4S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 58786.180 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, UniProt: O24243*PLUS | ||||||||||
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#2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-FAD / | #4: Chemical | ChemComp-HBX / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | Sequence details | M532 is maybe a natural mutagenesis of the AOA5E4GBK6 since authors have confirmed that the initial ...M532 is maybe a natural mutagenesis of the AOA5E4GBK6 since authors have confirmed that the initial sequence which was amplified by PCR reaction from the cDNA library of the Prunus communis. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.24 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: Tris-bicine, 100 mM, pH 8.5; CaCl2, 60 mM; MgCl2, 60 mM; PEG 500MME, 20%, v/v; PEG 20000, 10%, w/v |
-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: Jun 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.598→50 Å / Num. obs: 79552 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 20.52 Å2 / CC1/2: 0.988 / Net I/σ(I): 48.5 |
Reflection shell | Resolution: 1.6→1.63 Å / Num. unique obs: 79552 / CC1/2: 0.954 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EB4 Resolution: 1.598→46.35 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.89
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.5 Å2 / Biso mean: 24.0342 Å2 / Biso min: 13.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.598→46.35 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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