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Yorodumi- PDB-3cxu: Structure of a Y149F mutant of epoxide hydrolase from Solanum tub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cxu | ||||||
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Title | Structure of a Y149F mutant of epoxide hydrolase from Solanum tuberosum | ||||||
Components | Epoxide hydrolase | ||||||
Keywords | HYDROLASE / EPOXIDE HYDROLASE / ALPHA/BETA HYDROLASE FOLD / Y149F / PROTON WIRE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Solanum tuberosum (potato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Naworyta, A. / Mowbray, S.L. / Widersten, M. / Thomaeus, A. | ||||||
Citation | Journal: Protein Sci. / Year: 2008 Title: Removal of distal protein-water hydrogen bonds in a plant epoxide hydrolase increases catalytic turnover but decreases thermostability Authors: Thomaeus, A. / Naworyta, A. / Mowbray, S.L. / Widersten, M. #1: Journal: Protein Sci. / Year: 2006 Title: X-ray structure of potato epoxide hydrolase sheds light on substrate specificity in plant enzymes Authors: Mowbray, S.L. / Elfstrom, L.T. / Ahlgren, K.M. / Andersson, C.E. / Widersten, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cxu.cif.gz | 152.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cxu.ent.gz | 117.7 KB | Display | PDB format |
PDBx/mmJSON format | 3cxu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/3cxu ftp://data.pdbj.org/pub/pdb/validation_reports/cx/3cxu | HTTPS FTP |
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-Related structure data
Related structure data | 2cjpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37139.551 Da / Num. of mol.: 2 / Mutation: Y149F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum tuberosum (potato) / Strain: Lehmi Russet / Plasmid: pGTacStEH1-5H-Y149F / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q41415, soluble epoxide hydrolase #2: Chemical | ChemComp-PG4 / | #3: 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: 2.29 Å3/Da / Density % sol: 46.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% PEG 10000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2007 / Details: Single Silicon (111) monochromator |
Radiation | Monochromator: Single Silicon (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 45424 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 8 / Num. unique all: 27087 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Starting model: PDB entry 2cjp Resolution: 2→19.976 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.187 / SU B: 3.206 / SU ML: 0.092 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.152 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.65 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.976 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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