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Yorodumi- PDB-8bhh: The crystal structure of a feruloyl esterase C from Fusarium oxys... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bhh | |||||||||
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Title | The crystal structure of a feruloyl esterase C from Fusarium oxysporum in complex with p-coumaric acid | |||||||||
Components | Carboxylic ester hydrolase | |||||||||
Keywords | HYDROLASE / ferulic acid esterase / coummaric acid / tannase-like / feruloyl 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 / 4'-HYDROXYCINNAMIC ACID / DI(HYDROXYETHYL)ETHER / Carboxylic ester hydrolase Function and homology information | |||||||||
Biological species | Fusarium oxysporum (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | |||||||||
Authors | Dimarogona, M. / Topakas, E. / Kosinas, C. / Ferousi, C. / Nikolaivits, E. | |||||||||
Funding support | Greece, European Union, 2items
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Citation | Journal: Febs Lett. / Year: 2023 Title: Crystal structure of the Fusarium oxysporum tannase-like feruloyl esterase FaeC in complex with p-coumaric acid provides insight into ligand binding. Authors: Ferousi, C. / Kosinas, C. / Nikolaivits, E. / Topakas, E. / Dimarogona, M. #1: Journal: Acta Crystallogr D Struct Biol / Year: 2023 Title: Structure-function studies of a novel laccase-like multicopper oxidase from Thermothelomyces thermophila provide insights into its biological role. Authors: Kosinas, C. / Zerva, A. / Topakas, E. / Dimarogona, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bhh.cif.gz | 249 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bhh.ent.gz | 195.6 KB | Display | PDB format |
PDBx/mmJSON format | 8bhh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bhh_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 8bhh_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 8bhh_validation.xml.gz | 51 KB | Display | |
Data in CIF | 8bhh_validation.cif.gz | 75.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/8bhh ftp://data.pdbj.org/pub/pdb/validation_reports/bh/8bhh | HTTPS FTP |
-Related structure data
Related structure data | 6fatS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 56143.637 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 , 3 types, 8 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-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 | Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 7 types, 908 molecules
#4: Chemical | #6: Chemical | ChemComp-EDO / #7: Chemical | #8: Chemical | ChemComp-PG4 / | #9: Chemical | ChemComp-P6G / | #10: Chemical | ChemComp-PEG / | #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.09 Å3/Da / Density % sol: 60.23 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: PEG400, Tris HCl pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97624 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97624 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→113.51 Å / Num. obs: 105053 / % possible obs: 69.5 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.69→1.835 Å / Num. unique obs: 5255 / CC1/2: 0.594 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FAT Resolution: 1.69→113.51 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.564 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.129 / 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: 28.708 Å2
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Refinement step | Cycle: 1 / Resolution: 1.69→113.51 Å
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