+Open data
-Basic information
Entry | Database: PDB / ID: 3yas | ||||||
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Title | HYDROXYNITRILE LYASE COMPLEXED WITH ACETONE | ||||||
Components | PROTEIN (HYDROXYNITRILE LYASE) | ||||||
Keywords | LYASE / OXYNITRILASE / CYANOGENESIS / CYANOHYDRIN FORMATION | ||||||
Function / homology | Function and homology information (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 | Hevea brasiliensis (rubber tree) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Zuegg, J. / Wagner, U.G. / Gugganig, M. / Kratky, C. | ||||||
Citation | 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. #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: 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. #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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3yas.cif.gz | 73.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3yas.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 3yas.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3yas_validation.pdf.gz | 383 KB | Display | wwPDB validaton report |
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Full document | 3yas_full_validation.pdf.gz | 384.3 KB | Display | |
Data in XML | 3yas_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 3yas_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/3yas ftp://data.pdbj.org/pub/pdb/validation_reports/ya/3yas | HTTPS FTP |
-Related structure data
Related structure data | 2yasC 4yasC 5yasC 6yasC 7yasC 1yasS 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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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.) Hevea brasiliensis (rubber tree) / Gene: HNL / Organ: LEAF / Plasmid: BHIL-D2 / Gene (production host): HNL / Production host: Pichia pastoris (fungus) / References: UniProt: P52704, EC: 4.1.2.39 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ACN / | #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: 2.75 Å3/Da / Density % sol: 55.3 % | ||||||||||||||||||||
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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 SOAKING CONDITIONS: 400 MM ACETONE SOLUTION. | ||||||||||||||||||||
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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.9 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→16 Å / Num. obs: 27904 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 7 Å2 / Rsym value: 0.096 / Net I/σ(I): 7.3 |
Reflection | *PLUS % possible obs: 99 % / Rmerge(I) obs: 0.091 |
Reflection shell | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 1.95 Å / % possible obs: 99 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YAS Resolution: 1.85→16 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 9.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.92 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 9.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.263 / % reflection Rfree: 4.2 % / Rfactor Rwork: 0.249 |