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Yorodumi- PDB-6fat: The crystal structure of a feruloyl esterase C from Fusarium oxys... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fat | |||||||||
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Title | The crystal structure of a feruloyl esterase C from Fusarium oxysporum. | |||||||||
Components | Carboxylic ester hydrolaseCarboxylesterase | |||||||||
Keywords | HYDROLASE / ferulic acid esterase | |||||||||
Function / homology | Tannase/feruloyl esterase / Tannase and feruloyl esterase / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / metal ion binding / Carboxylic ester hydrolase Function and homology information | |||||||||
Biological species | Fusarium oxysporum (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Dimarogona, M. / Chrysina, E.D. | |||||||||
Funding support | Greece, 2items
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Citation | Journal: Febs Lett. / Year: 2020 Title: The crystal structure of a Fusarium oxysporum feruloyl esterase that belongs to the tannase family Authors: Dimarogona, M. / Topakas, E. / Christakopoulos, P. / Chrysina, E.D. #1: Journal: Appl. Microbiol. Biotechnol. / Year: 2008 Title: Cloning, characterization and functional expression of an alkalitolerant type C feruloyl esterase from Fusarium oxysporum. Authors: Moukouli, M. / Topakas, E. / Christakopoulos, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fat.cif.gz | 225 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fat.ent.gz | 178.3 KB | Display | PDB format |
PDBx/mmJSON format | 6fat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/6fat ftp://data.pdbj.org/pub/pdb/validation_reports/fa/6fat | HTTPS FTP |
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-Related structure data
Related structure data | 3wmtS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 58516.184 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusarium oxysporum (fungus) / Gene: faeC / Production host: Komagataella pastoris (fungus) References: UniProt: A0A1D3S5H0, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases |
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-Sugars , 6 types, 8 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Sugar | |
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-Non-polymers , 2 types, 359 molecules
#8: Chemical | #9: 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: 2.57 Å3/Da / Density % sol: 52.23 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 30% (v/v) PEG400, 0.1M Tris-HCl pH 8.5 buffer |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.2395 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jan 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2395 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→102.35 Å / Num. obs: 52149 / % possible obs: 98.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 0.095 |
Reflection shell | Resolution: 2.3→2.37 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WMT Resolution: 2.3→102.35 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.882 / SU ML: 0.218 / Cross valid method: FREE R-VALUE / ESU R: 0.373 / ESU R Free: 0.231 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.961 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→102.35 Å
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Refine LS restraints |
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