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Yorodumi- PDB-5z7j: Crystal structure of a lactonase double mutant in complex with li... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z7j | ||||||
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Title | Crystal structure of a lactonase double mutant in complex with ligand l | ||||||
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-36J / DI(HYDROXYETHYL)ETHER / 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: 1.98 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 | 5z7j.cif.gz | 450.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z7j.ent.gz | 368.1 KB | Display | PDB format |
PDBx/mmJSON format | 5z7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/5z7j ftp://data.pdbj.org/pub/pdb/validation_reports/z7/5z7j | HTTPS FTP |
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-Related structure data
Related structure data | 5xo6C 5xo7C 5xo8C 5z5jC 5z97C 5ie4S 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 29154.854 Da / Num. of mol.: 8 / Fragment: UNP residues 3-266 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhinocladiella mackenziei CBS 650.93 (fungus) Gene: Z518_04590 / Plasmid: pET-46 EK/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D2ILK1 #2: Chemical | ChemComp-36J / ( #3: Chemical | #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: 3.07 Å3/Da / Density % sol: 59.94 % / Mosaicity: 0.908 ° |
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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 and 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: 1.98→25 Å / Num. obs: 188099 / % possible obs: 97.7 % / Redundancy: 4 % / Biso Wilson estimate: 30.94 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.042 / Rrim(I) all: 0.085 / Χ2: 0.705 / Net I/σ(I): 10.6 / Num. measured all: 752400 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.98→24.714 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 22.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.35 Å2 / Biso mean: 36.0956 Å2 / Biso min: 18.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.98→24.714 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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