+Open data
-Basic information
Entry | Database: PDB / ID: 5.0E+46 | ||||||
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Title | Hydroxynitrile lyase from the fern Davallia tyermanii | ||||||
Components | Hydroxynitrile lyase | ||||||
Keywords | LYASE / hydroxynitrile lyase / fern | ||||||
Function / homology | START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / lyase activity / 2-Layer Sandwich / Alpha Beta / Hydroxynitrile lyase Function and homology information | ||||||
Biological species | Davallia tyermannii (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.854 Å | ||||||
Authors | Pavkov-Keller, T. / Diepold, M. / Gruber, K. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Sci Rep / Year: 2017 Title: Enzyme discovery beyond homology: a unique hydroxynitrile lyase in the Bet v1 superfamily. Authors: Lanfranchi, E. / Pavkov-Keller, T. / Koehler, E.M. / Diepold, M. / Steiner, K. / Darnhofer, B. / Hartler, J. / Van Den Bergh, T. / Joosten, H.J. / Gruber-Khadjawi, M. / Thallinger, G.G. / ...Authors: Lanfranchi, E. / Pavkov-Keller, T. / Koehler, E.M. / Diepold, M. / Steiner, K. / Darnhofer, B. / Hartler, J. / Van Den Bergh, T. / Joosten, H.J. / Gruber-Khadjawi, M. / Thallinger, G.G. / Birner-Gruenberger, R. / Gruber, K. / Winkler, M. / Glieder, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e46.cif.gz | 92.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e46.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 5e46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/5e46 ftp://data.pdbj.org/pub/pdb/validation_reports/e4/5e46 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23541.344 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: GenBank asseccion number KT804569 / Source: (gene. exp.) Davallia tyermannii (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1C9V3S9*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.83 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Native crystals of DtHNL1 were obtained by mixing 0.5ul 4 mg/mL protein sample (in 10 mM Tris-HCl pH 8.0) with 1 ul reservoir solution (0.9 M NaNO3; Na2HPO4; (NH4)2SO4 mix, 0.1 M Tris-Bicine ...Details: Native crystals of DtHNL1 were obtained by mixing 0.5ul 4 mg/mL protein sample (in 10 mM Tris-HCl pH 8.0) with 1 ul reservoir solution (0.9 M NaNO3; Na2HPO4; (NH4)2SO4 mix, 0.1 M Tris-Bicine Buffer pH 8.5 and 30% (w/v) polyethylene glycol monomethyl ether 550 & polyethylene glycol 20k; Morpheus condition C9). Additionally, native crystals were also grown by mixing 1 ul 4 mg/mL protein sample (in 10 mM Tris-HCl pH 8.0) with 0.5ul reservoir solution (0.1 M 2-(4-(2-hydroxyethyl)-1-piperazinyl) ethanesulfonic acid pH 7.5 and 10% (w/v) polyethylene glycol; JSCG condition B4). SeMet-DtHNL1 crystals were obtained in 0.2 M sodium thiocyanate, 20% (w/v) polyethylene glycol 3350. A 1:1 ratio of protein and screening solutions was used, using protein concentration of 3 mg/mL (in 10 mM Tris-HCl pH 8.0). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→58 Å / Num. obs: 34750 / % possible obs: 99.84 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.188 / Net I/σ(I): 9.97 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 13 % / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 2.57 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.854→57.971 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.854→57.971 Å
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Refine LS restraints |
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LS refinement shell |
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