+Open data
-Basic information
Entry | Database: PDB / ID: 4nzz | ||||||
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Title | Crystal structure of epoxide hydrolase from bacillus megaterium | ||||||
Components | Soluble epoxide hydrolase | ||||||
Keywords | HYDROLASE / A/B HYDROLASE FOLD / EPOXIDE HYDROLASE | ||||||
Function / homology | Function and homology information pyrimidine-5'-nucleotide nucleosidase / pyrimidine-5'-nucleotide nucleosidase activity Similarity search - Function | ||||||
Biological species | Bacillus megaterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å | ||||||
Authors | Kong, X.D. / Zhou, J.H. / Xu, J.H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Engineering of an epoxide hydrolase for efficient bioresolution of bulky pharmaco substrates. Authors: Kong, X.D. / Yuan, S. / Li, L. / Chen, S. / Xu, J.H. / Zhou, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nzz.cif.gz | 138.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nzz.ent.gz | 108.7 KB | Display | PDB format |
PDBx/mmJSON format | 4nzz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nzz_validation.pdf.gz | 441.5 KB | Display | wwPDB validaton report |
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Full document | 4nzz_full_validation.pdf.gz | 448.6 KB | Display | |
Data in XML | 4nzz_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 4nzz_validation.cif.gz | 38.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/4nzz ftp://data.pdbj.org/pub/pdb/validation_reports/nz/4nzz | HTTPS FTP |
-Related 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: 37088.668 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / Strain: ECU1001 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: G9BEX6, pyrimidine-5'-nucleotide nucleosidase #2: 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: 1.99 Å3/Da / Density % sol: 38.12 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 8.5 Details: 0.5M LICL, 0.1M TRIS-HCL, 28% PEG 6000, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, EVAPORATION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 26, 2010 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.749→64.333 Å / Num. obs: 59760 / % possible obs: 99 % / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.75→1.81 Å / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.75→35.58 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 23.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.57 Å2 / ksol: 0.32 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.75→35.58 Å
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Refine LS restraints |
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LS refinement shell |
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