+Open data
-Basic information
Entry | Database: PDB / ID: 1yas | ||||||
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Title | HYDROXYNITRILE LYASE COMPLEXED WITH HISTIDINE | ||||||
Components | HYDROXYNITRILE LYASE | ||||||
Keywords | COMPLEX (LYASE/PEPTIDE) / OXYNITRILASE / CYANOGENESIS / CYANHYDRIN FORMATION / LYASE / COMPLEX (LYASE-PEPTIDE) / COMPLEX (LYASE-PEPTIDE) complex | ||||||
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 / MIR / Resolution: 1.9 Å | ||||||
Authors | Wagner, U.G. / Kratky, C. | ||||||
Citation | 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. #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: Acta Crystallogr.,Sect.D / Year: 1996 Title: Crystallization of a Hydroxynitrile Lyase Authors: Wagner, U.G. / Schall, M. / Hayn, M. / Hasslacher, M. / Schwab, H. / Griengl, H.S. / Kratky, C. #3: 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 | 1yas.cif.gz | 64.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yas.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 1yas.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yas_validation.pdf.gz | 397.2 KB | Display | wwPDB validaton report |
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Full document | 1yas_full_validation.pdf.gz | 401.7 KB | Display | |
Data in XML | 1yas_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 1yas_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/1yas ftp://data.pdbj.org/pub/pdb/validation_reports/ya/1yas | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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-HIS / |
#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: 56 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / pH: 7.5 Details: 0.1 M NATRIUM HEPES BUFFER PH=7.5 2 % PEG 400, 2.0 M AMMONIUM SULFATE, 20 DEGREES., temperature 293K | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: used to seeding | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.92 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 12, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→15 Å / Num. obs: 24031 / % possible obs: 90.4 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 15.29 Å2 / Rmerge(I) obs: 0.073 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.355 / % possible all: 67.8 |
Reflection | *PLUS Num. measured all: 137615 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.9→15 Å / Cross valid method: FREE-R / σ(F): 3
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Displacement parameters | Biso mean: 8.75 Å2
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Refine analyze | Luzzati d res low obs: 15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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