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Yorodumi- PDB-4oao: A mutant of Axe2 (R55A), and acetyl-xylooligosaccharide esterase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oao | ||||||
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Title | A mutant of Axe2 (R55A), and acetyl-xylooligosaccharide esterase from Geobacillus Stearmophilus | ||||||
Components | Acetyl xylan esterase | ||||||
Keywords | HYDROLASE / SGNH fold / Acetyl-xylooligosaccharide esterase | ||||||
Function / homology | Function and homology information acetylxylan esterase / acetylxylan esterase activity / xylan catabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Lansky, S. / Alalouf, O. / Solomon, H.V. / Belrhali, H. / Shoham, Y. / Shoham, G. | ||||||
Citation | Journal: To be Published Title: A mutant of Axe2 (R55A), and acetyl-xylooligosaccharide esterase from Geobacillus Stearmophilus Authors: Lansky, S. / Alalouf, O. / Solomon, H.V. / Belrhali, H. / Shoham, Y. / Shoham, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oao.cif.gz | 108.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oao.ent.gz | 84.2 KB | Display | PDB format |
PDBx/mmJSON format | 4oao.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/4oao ftp://data.pdbj.org/pub/pdb/validation_reports/oa/4oao | HTTPS FTP |
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-Related structure data
Related structure data | 3w7vS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24714.410 Da / Num. of mol.: 2 / Mutation: R55A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: axe2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09LX1 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: 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: 3.2 Å3/Da / Density % sol: 61.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 1.2M potassium sodium tartrate, 0.1M imidazole buffer, pH 7.8, 0.3M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 11, 2013 |
Radiation | Monochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→38 Å / Num. all: 39198 / Num. obs: 39198 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Rmerge(I) obs: 0.118 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 13 % / Rmerge(I) obs: 0.426 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3W7V Resolution: 2.05→38 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.699 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.111 / 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: 29.766 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→38 Å
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Refine LS restraints |
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