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Yorodumi- PDB-5z97: Crystal structure of a lactonase double mutant in complex with li... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z97 | ||||||
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Title | Crystal structure of a lactonase double mutant in complex with ligand N | ||||||
Components | Lactonase for protein | ||||||
Keywords | HYDROLASE / ALPHA/BETA-HYDROLASE / LACTONASE / ZEARALENONE | ||||||
Function / homology | alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / Chem-ZER / AB hydrolase-1 domain-containing protein Function and homology information | ||||||
Biological species | Rhinocladiella mackenziei CBS 650.93 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Zheng, Y.Y. / Liu, W.D. / Chen, C.C. / Guo, R.T. | ||||||
Funding support | China, 1items
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Citation | Journal: Acs Catalysis / Year: 2018 Title: Crystal Structure of a Mycoestrogen-Detoxifying Lactonase from Rhinocladiella mackenziei: Molecular Insight into ZHD Substrate Selectivity Authors: Zheng, Y.Y. / Liu, W.T. / Chen, C.C. / Hu, X.Y. / Liu, W.D. / Ko, T.P. / Tang, X.K. / Wei, H.L. / Huang, J.W. / 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 | 5z97.cif.gz | 218.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z97.ent.gz | 175.5 KB | Display | PDB format |
PDBx/mmJSON format | 5z97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/5z97 ftp://data.pdbj.org/pub/pdb/validation_reports/z9/5z97 | HTTPS FTP |
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-Related structure data
Related structure data | 5xo6C 5xo7C 5xo8C 5z5jC 5z7jC 5ie4S 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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-Components
#1: Protein | Mass: 29083.775 Da / Num. of mol.: 4 / Fragment: UNP residues 4-266 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhinocladiella mackenziei CBS 650.93 (fungus) Plasmid: pET-46 EK/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D2ILK1 #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: 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: 2.65 Å3/Da / Density % sol: 53.58 % / Mosaicity: 0.656 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Ammonium Sulfate, 0.085M Sodium Cacodylate pH 6.5, 25-28%(w/v) Polyethylene Glycol 8000, 15%(v/v) Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Aug 2, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.32→25 Å / Num. obs: 50048 / % possible obs: 95 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.038 / Rrim(I) all: 0.077 / Χ2: 1.083 / Net I/σ(I): 12.6 / Num. measured all: 194860 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IE4 Resolution: 2.32→25 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.897 / SU B: 9.166 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.398 / ESU R Free: 0.27 / 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: 48.23 Å2
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Refinement step | Cycle: 1 / Resolution: 2.32→25 Å
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Refine LS restraints |
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