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Open data
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Basic information
Entry | Database: PDB / ID: 7yas | ||||||
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Title | HYDROXYNITRILE LYASE, LOW TEMPERATURE NATIVE STRUCTURE | ||||||
![]() | PROTEIN (HYDROXYNITRILE LYASE) | ||||||
![]() | LYASE / OXYNITRILASE / CYANOGENESIS / CYANHYDRIN FORMATION / COMPLEX (LYASE-PEPTIDE) | ||||||
Function / homology | ![]() (S)-hydroxynitrile lyase / aliphatic (S)-hydroxynitrile lyase activity / aromatic (S)-hydroxynitrile lyase activity / jasmonic acid metabolic process / methyl salicylate esterase activity / methyl jasmonate esterase activity / salicylic acid metabolic process / methyl indole-3-acetate esterase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zuegg, J. / Wagner, U.G. / Gugganig, M. / Kratky, C. | ||||||
![]() | ![]() Title: Three-dimensional structures of enzyme-substrate complexes of the hydroxynitrile lyase from Hevea brasiliensis. Authors: Zuegg, J. / Gruber, K. / Gugganig, M. / Wagner, U.G. / Kratky, C. #1: Journal: Proteins / Year: 1997 Title: Hydroxynitrile Lyase from Hevea brasiliensis: Molecular Characterization and Mechanism of Enzyme Catalysis Authors: Hasslacher, M. / Kratky, C. / Griengl, H. / Schwab, H. / Kohlwein, S.D. #2: ![]() Title: Mechanism of Cyanogenesis: The Crystal Structure of Hydroxynitrile Lyase from Hevea brasiliensis Authors: Wagner, U.G. / Hasslacher, M. / Griengl, H. / Schwab, H. / Kratky, C. #3: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Crystallization and preliminary X-ray diffraction studies of a hydroxynitrile lyase from Hevea brasiliensis. Authors: Wagner, U.G. / Schall, M. / Hasslacher, M. / Hayn, M. / Griengl, H. / Schwab, H. / Kratky, C. #4: Journal: J.Biol.Chem. / Year: 1996 Title: Molecular Cloning of the Full-Length Cdna of (S)-Hydroxynitrile Lyase from Hevea brasiliensis. Functional Expression in Escherichia coli and Saccharomyces cerevisiae and Identification of an Active Site Residue Authors: Hasslacher, M. / Schall, M. / Hayn, M. / Griengl, H. / Kohlwein, S.D. / Schwab, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.7 KB | Display | ![]() |
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PDB format | ![]() | 53.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 393.8 KB | Display | ![]() |
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Full document | ![]() | 395.2 KB | Display | |
Data in XML | ![]() | 7.2 KB | Display | |
Data in CIF | ![]() | 12.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yasC ![]() 3yasC ![]() 4yasC ![]() 5yasC ![]() 6yasC ![]() 1yasS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 29262.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-EPE / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 0.1 M NATRIUM HEPES BUFFER PH=7.5 2 % PEG 400, 2.0 M AMMONIUM SULFATE, 20 DEGREES. | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→28 Å / Num. obs: 30389 / % possible obs: 91.6 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rsym value: 0.037 / Net I/σ(I): 16 |
Reflection | *PLUS Rmerge(I) obs: 0.037 |
Reflection shell | *PLUS Highest resolution: 1.75 Å / Lowest resolution: 1.81 Å / % possible obs: 97.8 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 6.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1YAS Resolution: 1.75→28 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: FREE-R / σ(F): 0
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Displacement parameters | Biso mean: 11.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.83 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 28 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.191 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 11.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.232 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.233 |