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- PDB-1dwq: Crystal Structure of Hydroxynitrile Lyase from Manihot esculenta ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dwq | ||||||
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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 | ||||||
![]() | HYDROXYNITRILE LYASE | ||||||
![]() | HYDROXYNITRILE LYASE / ![]() | ||||||
Function / homology | ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lauble, H. / Forster, S. / Mielich, B. / Wajant, H. / Effenberger, F. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115 KB | Display | ![]() |
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PDB format | ![]() | 94.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | BIOLOGICAL_UNIT: TETRAMER |
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Components
#1: Protein | Mass: 29891.271 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: CHLOROACETONE COMPLEX / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ATO / | ![]() #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: ![]() |
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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: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→20 Å / Num. obs: 54130 / % possible obs: 96.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.055 / Rsym value: 0.074 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.1 / % possible all: 98.2 |
Reflection | *PLUS Num. measured all: 207542 / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS % possible obs: 98.2 % / Rmerge(I) obs: 0.159 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Displacement parameters | Biso mean: 33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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