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Yorodumi- PDB-5ie4: Crystal structure of a lactonase mutant in complex with substrate a -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ie4 | ||||||
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Title | Crystal structure of a lactonase mutant in complex with substrate a | ||||||
Components | Zearalenone hydrolase | ||||||
Keywords | HYDROLASE / ALPHA/BETA-HYDROLASE / LACTONASE / ZEARALENONE | ||||||
Function / homology | alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Chem-36J / Zearalenone hydrolase Function and homology information | ||||||
Biological species | Clonostachys rosea (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å | ||||||
Authors | Zheng, Y.Y. / Xu, Z.X. / Liu, W.D. / Chen, C.C. / Guo, R.T. | ||||||
Citation | Journal: Acs Catalysis / Year: 2016 Title: Enhanced alph-Zearalenol Hydrolyzing Activity of a Mycoestrogen-Detoxifying Lactonase by Structure-Based Engineering Authors: Xu, Z.X. / Liu, W.D. / Chen, C.C. / Li, Q. / Huang, J.W. / Ko, T.P. / Liu, G. / Liu, W. / Peng, W. / Cheng, Y.S. / Chen, Y. / Jin, J. / Li, H. / Zheng, Y.Y. / Guo, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ie4.cif.gz | 147.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ie4.ent.gz | 115.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ie4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/5ie4 ftp://data.pdbj.org/pub/pdb/validation_reports/ie/5ie4 | HTTPS FTP |
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-Related structure data
Related structure data | 5ie5C 5ie6C 5ie7C 3wzlS C: citing same article (ref.) 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 1 - 264 / Label seq-ID: 1 - 264
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-Components
#1: Protein | Mass: 28762.627 Da / Num. of mol.: 3 / Mutation: S102A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clonostachys rosea (fungus) / Gene: zhd101 / Plasmid: pET-46 EK/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NKB0 #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: 2.94 Å3/Da / Density % sol: 58.18 % / Mosaicity: 0.613 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 24% PEG 2000 MME, 0.1M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97622 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→25 Å / Num. obs: 26370 / % possible obs: 97.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.024 / Rrim(I) all: 0.059 / Χ2: 1.205 / Net I/av σ(I): 36.758 / Net I/σ(I): 13.9 / Num. measured all: 162671 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WZL Resolution: 2.8→25 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.875 / SU B: 22.212 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.751 / ESU R Free: 0.354 / 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: 36.008 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→25 Å
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Refine LS restraints |
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