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Yorodumi- PDB-5mif: Crystal structure of carboxyl esterase 2 (TmelEST2) from mycorrhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mif | ||||||
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Title | Crystal structure of carboxyl esterase 2 (TmelEST2) from mycorrhizal fungus Tuber melanosporum | ||||||
Components | 'Carboxyl esterase 2 | ||||||
Keywords | HYDROLASE / lipase alpha/beta hydrolase fold archaebacterial-like enzymes | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Tuber melanosporum Mel28 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.141 Å | ||||||
Authors | Zanotti, G. / Vallese, F. / Cavazzini, D. / Ottonello, S. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: A family of archaea-like carboxylesterases preferentially expressed in the symbiotic phase of the mycorrhizal fungus Tuber melanosporum. Authors: Cavazzini, D. / Grossi, G. / Levati, E. / Vallese, F. / Montanini, B. / Bolchi, A. / Zanotti, G. / Ottonello, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mif.cif.gz | 254.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mif.ent.gz | 204.6 KB | Display | PDB format |
PDBx/mmJSON format | 5mif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mif_validation.pdf.gz | 958.5 KB | Display | wwPDB validaton report |
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Full document | 5mif_full_validation.pdf.gz | 982.5 KB | Display | |
Data in XML | 5mif_validation.xml.gz | 50.8 KB | Display | |
Data in CIF | 5mif_validation.cif.gz | 72.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/5mif ftp://data.pdbj.org/pub/pdb/validation_reports/mi/5mif | 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 on special symmetry positions |
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-Components
#1: Protein | ' Mass: 37443.684 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tuber melanosporum Mel28 (fungus) / Gene: GSTUM_00003552001 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus RIL / References: UniProt: D5GA36 #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: 2.62 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 18 mg/ml in 25 mM Tris-HCl pH 8.0, 0.1M NaCl, 2% v/v Triton X-100) and 20% polyethylene glycol 3350 in 0.2 M KNO3 (pH 6.0) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→47.28 Å / Num. obs: 93001 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 71.46 |
Reflection shell | Resolution: 2.14→2.26 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 3.3 / % possible all: 98.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: in house Resolution: 2.141→47.276 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.95
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.141→47.276 Å
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Refine LS restraints |
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LS refinement shell |
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