+
Open data
-
Basic information
Entry | Database: PDB / ID: 4yas | ||||||
---|---|---|---|---|---|---|---|
Title | HYDROXYNITRILE LYASE COMPLEXED WITH CHLORALHYDRATE | ||||||
![]() | PROTEIN (HYDROXYNITRILE LYASE) | ||||||
![]() | LYASE / OXYNITRILASE / CYANOGENESIS / CYANOHYDRIN 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 | ![]() ![]() ![]() | ||||||
![]() | Zuegg, J. / Wagner, U.G. / 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: 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: ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 72.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 52.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 385.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 386.8 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 11.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yasC ![]() 3yasC ![]() 5yasC ![]() 6yasC ![]() 7yasC ![]() 1yasS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 | ![]()
| ||||||||||||
3 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 29262.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-CLX / | #4: Water | ChemComp-HOH / | Nonpolymer details | COVALENTLY | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.6 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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: 5 MM CHLORAL HYDRATE SOLUTION. | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 98 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→36 Å / Num. obs: 26753 / % possible obs: 81.5 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 4.3 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 6.4 |
Reflection | *PLUS % possible obs: 93.6 % |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 100 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 6.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1YAS Resolution: 2→15 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.187 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 8.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.255 / % reflection Rfree: 5.5 % / Rfactor Rwork: 0.196 |