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Yorodumi- PDB-1e8d: MECHANISTIC ASPECTS OF CYANOGENESIS FROM ACTIVE SITE MUTANT SER80... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e8d | ||||||
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Title | MECHANISTIC ASPECTS OF CYANOGENESIS FROM ACTIVE SITE MUTANT SER80ALA OF HYDROXYNITRILE LYASE FROM MANIHOT ESCULENTA IN COMPLEX WITH ACETONE CYANOHYDRIN | ||||||
Components | HYDROXYNITRILE LYASE | ||||||
Keywords | LYASE / HYDROXYNITRILE LYASE / ACTIVE SITE MUTANT / ACETONE CYANOHYDRIN 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. / Miehlich, B. / Foerster, S. / Wajant, H. / Effenberger, F. | ||||||
Citation | Journal: Protein Sci. / Year: 2001 Title: Mechanistic Aspects of Cyanogenesis from Active-Site Mutant Ser80Ala of Hydroxynitrile Lyase from Manihot Esculenta in Complex with Acetone Cyanohydrin. Authors: Lauble, H. / Miehlich, B. / Forster, S. / Wajant, H. / Effenberger, F. #1: 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. / Foerster, 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 | 1e8d.cif.gz | 121.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e8d.ent.gz | 94.7 KB | Display | PDB format |
PDBx/mmJSON format | 1e8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e8d_validation.pdf.gz | 437.5 KB | Display | wwPDB validaton report |
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Full document | 1e8d_full_validation.pdf.gz | 447.9 KB | Display | |
Data in XML | 1e8d_validation.xml.gz | 24 KB | Display | |
Data in CIF | 1e8d_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/1e8d ftp://data.pdbj.org/pub/pdb/validation_reports/e8/1e8d | HTTPS FTP |
-Related structure data
Related structure data | 1e89SC 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: 29819.209 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ACETONE CYANOHYDRIN COMPLEX / Source: (gene. exp.) MANIHOT ESCULENTA (cassava) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P52705, EC: 4.2.1.37 #2: Chemical | ChemComp-CNH / #3: Water | ChemComp-HOH / | Compound details | CHAIN A, B: CONTAINS ENGINEERED | |
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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: 4.5 Å3/Da / Density % sol: 71 % | |||||||||||||||||||||||||
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Crystal grow | pH: 4.8 / Details: 0.1 M NA CITRATE, PH 4.8, 6% PEG8000, 28% MPD | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: Lauble, H., (1999) Acta Crystallogr.,Sect.D, 55, 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→15 Å / Num. obs: 52736 / % possible obs: 97.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.068 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.135 / % possible all: 98.5 |
Reflection | *PLUS Num. measured all: 211247 / Rmerge(I) obs: 0.068 |
Reflection shell | *PLUS % possible obs: 98.5 % / Rmerge(I) obs: 0.135 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E89 Resolution: 2.2→8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 25.5 Å2
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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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LS refinement shell | Resolution: 2.2→2.33 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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