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Yorodumi- PDB-1yb7: Hydroxynitrile lyase from hevea brasiliensis in complex with 2,3-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yb7 | ||||||
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Title | Hydroxynitrile lyase from hevea brasiliensis in complex with 2,3-dimethyl-2-hydroxy-butyronitrile | ||||||
Components | (S)-acetone-cyanohydrin lyase | ||||||
Keywords | LYASE / ALPHA-BETA HYDROLASE FOLD / SUBSTRATE COMPLEX / CATALYTIC TRIAD | ||||||
Function / homology | Function and homology information (S)-hydroxynitrile lyase / aliphatic (S)-hydroxynitrile lyase activity / aromatic (S)-hydroxynitrile lyase activity Similarity search - Function | ||||||
Biological species | Hevea brasiliensis (rubber tree) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.76 Å | ||||||
Authors | Gruber, K. / Gartler, G. / Kratky, C. | ||||||
Citation | Journal: J.Biotechnol. / Year: 2007 Title: Structural determinants of the enantioselectivity of the hydroxynitrile lyase from Hevea brasiliensis Authors: Gartler, G. / Kratky, C. / Gruber, K. #1: Journal: J.Biol.Chem. / Year: 2004 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. #2: Journal: Biol.Chem. / Year: 1999 Title: Atomic Resolution Crystal Structure of Hydroxynitrile Lyase from Hevea Brasiliensis Authors: Gruber, K. / Gugganig, M. / Wagner, U.G. / Kratky, C. #3: Journal: Protein Sci. / Year: 1999 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. #4: Journal: Structure / Year: 1996 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yb7.cif.gz | 72.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yb7.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 1yb7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/1yb7 ftp://data.pdbj.org/pub/pdb/validation_reports/yb/1yb7 | HTTPS FTP |
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-Related structure data
Related structure data | 1yb6C 2yasS 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: 29131.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hevea brasiliensis (rubber tree) / Tissue: LEAF / Gene: HNL / Plasmid: BHIL-D2 / Production host: Pichia pastoris (fungus) / References: UniProt: P52704, EC: 4.1.2.39 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ICN / ( | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: AMMONIUM SULFATE, PEG 400, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9101 / Wavelength: 0.9101 Å |
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: 0.9101 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→40.98 Å / Num. all: 31024 / Num. obs: 31024 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.062 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 1.76→1.82 Å / Mean I/σ(I) obs: 4.4 / Rsym value: 0.128 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2YAS Resolution: 1.76→40.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1841708.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.7102 Å2 / ksol: 0.37273 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.76→40.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.82 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
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Xplor file |
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