+Open data
-Basic information
Entry | Database: PDB / ID: 4y9s | ||||||
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Title | structure of an H300N mutant of potato epoxide hydrolase, StEH1 | ||||||
Components | Epoxide hydrolase | ||||||
Keywords | HYDROLASE / mutation of catalytic residue | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Solanum tuberosum (potato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Naworyta, A. / Mowbray, S.L. / Widersten, M. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: ACS Catal / Year: 2015 Title: Expanding the Catalytic Triad in Epoxide Hydrolases and Related Enzymes. Authors: Amrein, B.A. / Bauer, P. / Duarte, F. / Janfalk Carlsson, A. / Naworyta, A. / Mowbray, S.L. / Widersten, M. / Kamerlin, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y9s.cif.gz | 148 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y9s.ent.gz | 116.4 KB | Display | PDB format |
PDBx/mmJSON format | 4y9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/4y9s ftp://data.pdbj.org/pub/pdb/validation_reports/y9/4y9s | 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37131.508 Da / Num. of mol.: 2 / Mutation: H300N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum tuberosum (potato) / Plasmid: pGTacStEH1-5H / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q41415 #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: 2.2 Å3/Da / Density % sol: 44.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: 1 UL DROPS OF PROTEIN SOLUTION (7.2 MG/ML, I.E. 0.2 MM, IN 30 MM TRIS-HCL, PH 7.4, 5 MM VALPROMIDE) WERE MIXED WITH 1 UL DROPS OF RESERVOIR SOLUTION (CONTAINING 90 MM NA-HEPES, PH 7.5, 25% ...Details: 1 UL DROPS OF PROTEIN SOLUTION (7.2 MG/ML, I.E. 0.2 MM, IN 30 MM TRIS-HCL, PH 7.4, 5 MM VALPROMIDE) WERE MIXED WITH 1 UL DROPS OF RESERVOIR SOLUTION (CONTAINING 90 MM NA-HEPES, PH 7.5, 25% PEG 10, 000). Once crystals were obtained they were soaked in mother liquor at pH 3.5 prior to freezing. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 18, 2008 / Details: toroidal mirror |
Radiation | Monochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2→51.36 Å / Num. obs: 45161 / % possible obs: 100 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2→2.09 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 4.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CJP Resolution: 2→51.36 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.353 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.956 Å2
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Refinement step | Cycle: LAST / Resolution: 2→51.36 Å
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Refine LS restraints |
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