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Yorodumi- PDB-3g0i: Complex of Aspergillus niger epoxide hydrolase with valpromide (2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g0i | ||||||
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Title | Complex of Aspergillus niger epoxide hydrolase with valpromide (2-propylpentanamide) | ||||||
Components | Epoxide hydrolase | ||||||
Keywords | HYDROLASE / Epoxide hydrolase / alpha/beta hydrolase fold / valpromide / 2-propylpentanamide | ||||||
Function / homology | Function and homology information epoxide hydrolase / epoxide metabolic process / epoxide hydrolase activity Similarity search - Function | ||||||
Biological species | Aspergillus niger (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Zou, J. / Mowbray, S.L. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: Directed evolution of an enantioselective epoxide hydrolase: uncovering the source of enantioselectivity at each evolutionary stage Authors: Reetz, M.T. / Bocola, M. / Wang, L.W. / Sanchis, J. / Cronin, A. / Arand, M. / Zou, J. / Archelas, A. / Bottalla, A.L. / Naworyta, A. / Mowbray, S.L. #1: Journal: Structure / Year: 2000 Title: Structure of Aspergillus niger epoxide hydrolase at 1.8 A resolution: implications for the structure and function of the mammalian microsomal class of epoxide hydrolases Authors: Zou, J. / Hallberg, B.M. / Bergfors, T. / Oesch, F. / Arand, M. / Mowbray, S.L. / Jones, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g0i.cif.gz | 170.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g0i.ent.gz | 136 KB | Display | PDB format |
PDBx/mmJSON format | 3g0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g0i_validation.pdf.gz | 442.9 KB | Display | wwPDB validaton report |
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Full document | 3g0i_full_validation.pdf.gz | 445.9 KB | Display | |
Data in XML | 3g0i_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 3g0i_validation.cif.gz | 47.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/3g0i ftp://data.pdbj.org/pub/pdb/validation_reports/g0/3g0i | HTTPS FTP |
-Related structure data
Related structure data | 3g02C 1qo7S 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
#1: Protein | Mass: 44124.180 Da / Num. of mol.: 2 / Fragment: UNP residues 5-396 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus niger (mold) / Strain: LCP521 / Gene: hyl1 / Plasmid: PGEF-ANEH336 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9UR30, microsomal epoxide hydrolase #2: Chemical | #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: 2.34 Å3/Da / Density % sol: 47.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% PEG6000, 0.1M MES, pH6.0, 0.1M unbuffered sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 1999 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. obs: 47596 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.066 / Χ2: 0.877 / Net I/σ(I): 16.947 |
Reflection shell | Resolution: 2.1→2.14 Å / Rmerge(I) obs: 0.213 / Num. unique all: 2189 / Χ2: 0.993 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QO7 Resolution: 2.1→38.21 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.231 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.179 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.58 Å2 / Biso mean: 14.057 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→38.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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