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- PDB-3fyt: Crystal structure of Bacillus pumilus acetyl xylan esterase S181A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fyt | |||||||||
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Title | Crystal structure of Bacillus pumilus acetyl xylan esterase S181A mutant in complex with beta-D-xylopyranose | |||||||||
![]() | Acetyl xylan esterase | |||||||||
![]() | HYDROLASE / alpha/beta hydrolase / carbohydrate esterase / CE7 / Bacillus pumilus | |||||||||
Function / homology | ![]() acetylesterase / polysaccharide metabolic process / acetylesterase activity Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Krastanova, I. / Cassetta, A. / Lamba, D. | |||||||||
![]() | ![]() Title: Structural and functional studies of Bacillus pumilus acetyl xylan esterase Authors: Krastanova, I. / Cassetta, A. / Mastihubova, M. / Biely, P. / Lamba, D. #1: ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 727.3 KB | Display | ![]() |
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PDB format | ![]() | 607 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 543 KB | Display | ![]() |
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Full document | ![]() | 584.1 KB | Display | |
Data in XML | ![]() | 127.3 KB | Display | |
Data in CIF | ![]() | 173.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3fvrSC ![]() 3fvtC ![]() 3fyuC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36098.844 Da / Num. of mol.: 12 / Mutation: S181A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CL / #3: Sugar | ChemComp-XYP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.63 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 6 Details: 0.20M lithium chloride, 0.13M D-xylose, 3% PEG 6000, 0.03M MES, pH 6.0, microbatch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 16, 2005 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→24.83 Å / Num. all: 100895 / Num. obs: 100895 / % possible obs: 77.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 37.66 Å2 / Rmerge(I) obs: 0.064 / Χ2: 1.117 |
Reflection shell | Resolution: 2.58→2.66 Å / Redundancy: 3 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4 / Num. unique all: 4985 / Χ2: 1.021 / % possible all: 50.1 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3FVR Resolution: 2.58→24.83 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: 39.298 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100 Å2 / Biso mean: 28.857 Å2 / Biso min: 5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.58→24.83 Å
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Refine LS restraints |
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Xplor file |
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