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- PDB-1sck: K236L mutant of hydroxynitrile lyase from Hevea brasiliensis in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1sck | ||||||
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Title | K236L mutant of hydroxynitrile lyase from Hevea brasiliensis in complex with acetone | ||||||
![]() | (S)-acetone-cyanohydrin lyase | ||||||
![]() | LYASE / alpha-beta hydrolase fold / substrate complex / catalytic triad | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Gruber, K. / Gartler, G. / Krammer, B. / Schwab, H. / Kratky, C. | ||||||
![]() | ![]() Title: Reaction mechanism of hydroxynitrile lyases of the alpha/beta-hydrolase superfamily: the three-dimensional structure of the transient enzyme-substrate complex certifies the crucial role of LYS236 Authors: Gruber, K. / Gartler, G. / Krammer, B. / Schwab, H. / Kratky, C. #1: ![]() Title: Atomic resolution crystal structure of hydroxynitrile lyase from hevea brasiliensis Authors: Gruber, K. / Gugganig, M. / Wagner, U.G. / Kratky, C. #2: ![]() 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. #3: ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.3 KB | Display | ![]() |
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PDB format | ![]() | 54.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.4 KB | Display | ![]() |
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Full document | ![]() | 442.1 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 21.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1sc9C ![]() 1sciC ![]() 1scqC ![]() 2yasS 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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1 | ![]()
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2 |
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Unit cell |
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Details | dimer; the second part of the biological assembly is generated by the two fod axis: x, -y+1, -z. |
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Components
#1: Protein | ( Mass: 29246.578 Da / Num. of mol.: 1 / Mutation: K236L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ACN / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.34 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium sulfate, PEG 400, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 12, 2000 |
Radiation | Monochromator: unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8452 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→13 Å / Num. all: 34698 / Num. obs: 34698 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.038 / Net I/σ(I): 30.5 |
Reflection shell | Resolution: 1.7→1.73 Å / Mean I/σ(I) obs: 7.9 / Num. unique all: 1738 / Rsym value: 0.198 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2yas Resolution: 1.7→11.91 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1795611.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: refinement against maximum likelihood target function
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.2782 Å2 / ksol: 0.439854 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→11.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.73 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 20
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Xplor file |
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