+Open data
-Basic information
Entry | Database: PDB / ID: 3wzl | ||||||
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Title | ZEN lactonase | ||||||
Components | Zearalenone hydrolase | ||||||
Keywords | HYDROLASE / alpha/beta-hydrolase / lactonase / zearalenone | ||||||
Function / homology | Function and homology information glycerolipid catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / triacylglycerol lipase activity Similarity search - Function | ||||||
Biological species | Clonostachys rosea (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Ko, T.P. / Huang, C.H. / Liu, J.R. / Guo, R.T. | ||||||
Citation | Journal: RSC ADV / Year: 2014 Title: Crystal structure and substrate-binding mode of the mycoestrogen-detoxifying lactonase ZHD from Clonostachys rosea Authors: Peng, W. / Ko, T.P. / Yang, Y. / Zheng, Y. / Chen, C.C. / Zhu, Z. / Huang, C.H. / Zeng, Y.F. / Huang, J.W. / Wand, A.H.-J. / Liu, J.R. / 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 | 3wzl.cif.gz | 320.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wzl.ent.gz | 265.3 KB | Display | PDB format |
PDBx/mmJSON format | 3wzl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/3wzl ftp://data.pdbj.org/pub/pdb/validation_reports/wz/3wzl | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / 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: 5 / Auth seq-ID: 1 - 264 / Label seq-ID: 15 - 278
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-Components
#1: Protein | Mass: 30498.426 Da / Num. of mol.: 3 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) / References: UniProt: Q8NKB0 #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: 2.81 Å3/Da / Density % sol: 56.17 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.5 Details: 24% PEG 2000 MME, 0.1M Bis-Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2013 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→25 Å / Num. all: 34045 / Num. obs: 33747 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 9.1 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 37.6 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 4.9 / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→24.98 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.897 / SU B: 22.924 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.567 / ESU R Free: 0.316 / 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 mean: 74.316 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→24.98 Å
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Refine LS restraints |
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