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- PDB-2yas: HYDROXYNITRILE LYASE FROM HEVEA BRASILIENSIS COMPLEXED WITH RHODANIDE -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yas | ||||||
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Title | HYDROXYNITRILE LYASE FROM HEVEA BRASILIENSIS COMPLEXED WITH RHODANIDE | ||||||
![]() | PROTEIN (HYDROXYNITRILE LYASE) | ||||||
![]() | LYASE / OXYNITRILASE / CYANOGENESIS / CYANHYDRIN FORMATION | ||||||
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. / 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: ![]() 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. #2: 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. #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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.8 KB | Display | ![]() |
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PDB format | ![]() | 53.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.7 KB | Display | ![]() |
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Full document | ![]() | 433.4 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3yasC ![]() 4yasC ![]() 5yasC ![]() 6yasC ![]() 7yasC ![]() 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 | ChemComp-SCN / | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: PH=7.5 2 % PEG 400, 2.0 M AMMONIUM SULFATE, 20 DEGREES. | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9076 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→14 Å / Num. obs: 34663 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.066 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.72→1.75 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 5.8 / Rsym value: 0.237 / % possible all: 99.6 |
Reflection | *PLUS Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 99.6 % / Rmerge(I) obs: 0.237 |
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Processing
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Refinement | Method to determine structure: OTHER Starting model: 1YAS Resolution: 1.72→14 Å / Num. parameters: 9757 / Num. restraintsaints: 8672 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28 (1995)53-56
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 2049 / Occupancy sum non hydrogen: 2411.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→14 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 14 Å / σ(F): 0 / % reflection Rfree: 11.1 % / Rfactor Rwork: 0.15 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |