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Yorodumi- PDB-1dwo: Crystal Structure of Hydroxynitrile Lyase from Manihot esculenta ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dwo | ||||||
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Title | Crystal Structure of Hydroxynitrile Lyase from Manihot esculenta in Complex with Substrates Acetone and Chloroacetone:Implications for the Mechanism of Cyanogenesis | ||||||
Components | HYDROXYNITRILE LYASE | ||||||
Keywords | HYDROXYNITRILE LYASE / ACETONE COMPLEX | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Lauble, H. / Forster, S. / Miehlich, B. / Wajant, H. / Effenberger, F. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Structure of Hydroxynitrile Lyase from Manihot Esculenta in Complex with Substrates Acetone and Chloroacetone: Implications for the Mechanism of Cyanogenesis Authors: Lauble, H. / Forster, S. / Miehlich, B. / Wajant, H. / Effenberger, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dwo.cif.gz | 115.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dwo.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 1dwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/1dwo ftp://data.pdbj.org/pub/pdb/validation_reports/dw/1dwo | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | BIOLOGICAL_UNIT: TETRAMER |
-Components
#1: Protein | Mass: 29835.209 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: ACETONE COMPLEX / Source: (gene. exp.) MANIHOT ESCULENTA (cassava) / Description: RECOMBINANT PROTEIN / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P52705, EC: 4.2.1.37 #2: Chemical | ChemComp-ACN / | #3: Water | ChemComp-HOH / | Sequence details | THE SWISSPROT ENTRY P52705 REPORTS THIS ENZYME TO BE EC 4.2.1.39, AND TO HAVE A HOMOTRIMERIC ...THE SWISSPROT ENTRY P52705 REPORTS THIS ENZYME TO BE EC 4.2.1.39, AND TO HAVE A HOMOTRIMER | |
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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: 4.3 Å3/Da / Density % sol: 71 % | |||||||||||||||||||||||||
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Crystal grow | pH: 5.4 / Details: 0.1 M NACITRAT, PH 5.4, 6% PEG8000, 28% MPD | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Lauble, H., (1999) Acta Crystallogr., D55, 904. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.905 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.905 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 52853 / % possible obs: 97.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.054 / Rsym value: 0.068 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.2 / % possible all: 99.4 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. measured all: 215742 / Rmerge(I) obs: 0.068 |
Reflection shell | *PLUS % possible obs: 99.4 % / Rmerge(I) obs: 0.141 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2
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Displacement parameters | Biso mean: 26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO |