+Open data
-Basic information
Entry | Database: PDB / ID: 3c6y | ||||||
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Title | HNL from Hevea brasiliensis to atomic resolution | ||||||
Components | Hydroxynitrilase | ||||||
Keywords | LYASE / atomic resolution / hydroxynitril lyase / catalysis / protonation state / ab initio calculations / substrate binding | ||||||
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 / molecular replacement/rigid body placement / Resolution: 1.25 Å | ||||||
Authors | Schmidt, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Atomic resolution crystal structures and quantum chemistry meet to reveal subtleties of hydroxynitrile lyase catalysis Authors: Schmidt, A. / Gruber, K. / Kratky, C. / Lamzin, V.S. #1: 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. #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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c6y.cif.gz | 190.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c6y.ent.gz | 154.4 KB | Display | PDB format |
PDBx/mmJSON format | 3c6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/3c6y ftp://data.pdbj.org/pub/pdb/validation_reports/c6/3c6y | HTTPS FTP |
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-Related structure data
Related structure data | 3c6xC 3c6zC 3c70C 1qj4S 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#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 / Plasmid: BHIL-D2 / Production host: Pichia pastoris (fungus) / References: UniProt: P52704, EC: 4.1.2.37 |
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-Non-polymers , 5 types, 541 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-BME / | #4: Chemical | ChemComp-ACN / | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-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: 55.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2% PEG400, 2M ammonium sulphate, 0.1M Hepes-Na, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8162 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 6, 2005 / Details: mirror |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8162 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→15 Å / Num. all: 83123 / Num. obs: 83123 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.25→1.26 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1596 / % possible all: 60 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement/rigid body placement Starting model: PDB ENTRY 1QJ4 Resolution: 1.25→15 Å / Num. parameters: 24616 / Num. restraintsaints: 30456 Cross valid method: FREE R initially, final refinement against all adata σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER / Details: full anisotropic refinement applied
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Displacement parameters | Biso mean: 13 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 34 / Occupancy sum hydrogen: 2013.38 / Occupancy sum non hydrogen: 2552.6 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→15 Å
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Refine LS restraints |
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