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Yorodumi- PDB-3fyu: Crystal structure of acetyl xylan esterase from Bacillus pumilus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fyu | |||||||||
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Title | Crystal structure of acetyl xylan esterase from Bacillus pumilus obtained in presence of D-xylose and sodium acetate | |||||||||
Components | (Acetyl xylan ...) x 3 | |||||||||
Keywords | HYDROLASE / alpha/beta hydrolase / carbohydrate esterase / CE7 / Bacillus pumilus | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Bacillus pumilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.62 Å | |||||||||
Authors | Krastanova, I. / Cassetta, A. / Lamba, D. | |||||||||
Citation | Journal: To be Published Title: Structural and functional studies of Bacillus pumilus acetyl xylan esterase Authors: Krastanova, I. / Cassetta, A. / Mastihubova, M. / Biely, P. / Lamba, D. #1: Journal: Biochim.Biophys.Acta / Year: 2005 Title: Heterologous expression, purification, crystallization, X-ray analysis and phasing of the acetyl xylan esterase from Bacillus pumilus Authors: Krastanova, I. / Guarnaccia, C. / Zahariev, S. / Degrassi, G. / Lamba, D. #2: Journal: Microbiology / Year: 2000 Title: The acetyl xylan esterase of Bacillus pumilus belongs to a family of esterases with broad substrate specificity Authors: Degrassi, G. / Kojic, M. / Ljubijankic, G. / Venturi, V. #3: Journal: Appl.Environ.Microbiol. / Year: 1998 Title: Purification and characterization of an acetyl xylan esterase from Bacillus pumilus Authors: Degrassi, G. / Okeke, B.C. / Bruschi, C.V. / Venturi, V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fyu.cif.gz | 743.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fyu.ent.gz | 616.7 KB | Display | PDB format |
PDBx/mmJSON format | 3fyu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/3fyu ftp://data.pdbj.org/pub/pdb/validation_reports/fy/3fyu | HTTPS FTP |
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-Related structure data
Related structure data | 3fvrC 3fvtSC 3fytC C: citing same article (ref.) 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
-Acetyl xylan ... , 3 types, 12 molecules AIBDHCEFGLMN
#1: Protein | Mass: 36156.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus pumilus (bacteria) / Strain: PS 213 / Gene: axe / Plasmid: pBPEB2 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q9K5F2, acetylesterase #2: Protein | Mass: 36174.895 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus pumilus (bacteria) / Strain: PS 213 / Gene: axe / Plasmid: pBPEB2 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q9K5F2, acetylesterase #3: Protein | Mass: 36114.844 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus pumilus (bacteria) / Strain: PS 213 / Gene: axe / Plasmid: pBPEB2 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q9K5F2, acetylesterase |
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-Sugars , 1 types, 7 molecules
#4: Sugar | ChemComp-XYP / |
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-Non-polymers , 4 types, 840 molecules
#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-ACY / #8: 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: 2.41 Å3/Da / Density % sol: 48.95 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 6 Details: 0.3M lithium chloride, 0.2M sodium acetate, 0.2M D-xylose, 5% PEG 6000, 0.05M MES, pH 6.0, microbatch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 15, 2004 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→30 Å / Num. all: 106905 / Num. obs: 106905 / % possible obs: 86.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 36.49 Å2 / Rmerge(I) obs: 0.097 / Χ2: 1.136 |
Reflection shell | Resolution: 2.62→2.72 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3.3 / Num. unique all: 8208 / Χ2: 1.028 / % possible all: 80.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3FVT Resolution: 2.62→26.88 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 14.674 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.86 Å2 / Biso mean: 19.338 Å2 / Biso min: 5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.62→26.88 Å
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Refine LS restraints |
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Xplor file |
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