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Yorodumi- PDB-4yk7: Crystal structure of S-hydroxynitrile lyase from Manihot esculent... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yk7 | ||||||
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Title | Crystal structure of S-hydroxynitrile lyase from Manihot esculenta (His103Leu) | ||||||
Components | (S)-hydroxynitrile lyase(S)-hydroxynitrile lyase | ||||||
Keywords | LYASE / S-hydroxynitrile lyase / hydrolase fold / His103Leu variant | ||||||
Function / homology | Function and homology information (S)-hydroxynitrile lyase / aliphatic (S)-hydroxynitrile lyase activity / aromatic (S)-hydroxynitrile lyase activity Similarity search - Function | ||||||
Biological species | Manihot esculenta (cassava) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å | ||||||
Authors | Dadashipour, M. / Nakano, S. / Asano, Y. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of S-hydroxynitrile lyase from Manihot esculenta (His103Leu) Authors: Dadashipour, M. / Nakano, S. / Asano, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yk7.cif.gz | 207.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yk7.ent.gz | 166.8 KB | Display | PDB format |
PDBx/mmJSON format | 4yk7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/4yk7 ftp://data.pdbj.org/pub/pdb/validation_reports/yk/4yk7 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 1 - 258 / Label seq-ID: 1 - 258
NCS ensembles :
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-Components
#1: Protein | ( Mass: 29383.691 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Manihot esculenta (cassava) / Gene: HNL / Production host: Escherichia coli (E. coli) / References: UniProt: P52705, (S)-hydroxynitrile lyase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.1M DL-Maleic acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→45.6 Å / Num. obs: 32186 / % possible obs: 100 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 34.6 |
Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 12.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.6→45.6 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.84 / SU B: 11.329 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.999 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→45.6 Å
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Refine LS restraints |
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