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Yorodumi- PDB-2dro: Crystal structure of reducing-end-xylose releasing exo-oligoxylan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dro | ||||||
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Title | Crystal structure of reducing-end-xylose releasing exo-oligoxylanase D263C mutant | ||||||
Components | Xylanase Y | ||||||
Keywords | HYDROLASE / (ALPLA/ALPHA)6 BARREL / GLYCOSIDE HYDROLASE FAMILY 8 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses | ||||||
Function / homology | Function and homology information oligosaccharide reducing-end xylanase / oligosaccharide reducing-end xylanase activity / xylan catabolic process Similarity search - Function | ||||||
Biological species | Bacillus halodurans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Fushinobu, S. / Hidaka, M. / Honda, Y. / Wakagi, T. / Shoun, H. / Kitaoka, M. | ||||||
Citation | Journal: J.Biochem. / Year: 2009 Title: Structural explanation for the acquisition of glycosynthase activity Authors: Hidaka, M. / Fushinobu, S. / Honda, Y. / Wakagi, T. / Shoun, H. / Kitaoka, M. #1: Journal: J.Biol.Chem. / Year: 2006 Title: The first glycosynthase derived from an inverting glycoside hydrolase Authors: Honda, Y. / Kitaoka, M. #2: Journal: J.Biol.Chem. / Year: 2005 Title: Structural basis for the specificity of the reducing end xylose-releasing exo-oligoxylanase from Bacillus halodurans C-125 Authors: Fushinobu, S. / Hidaka, M. / Honda, Y. / Wakagi, T. / Shoun, H. / Kitaoka, M. #3: Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Crystallization and preliminary X-ray analysis of reducing-end xylose-releasing exo-oligoxylanase from Bacillus halodurans C-125 Authors: Honda, Y. / Fushinobu, S. / Hidaka, M. / Wakagi, T. / Shoun, H. / Kitaoka, M. #4: Journal: J.Biol.Chem. / Year: 2004 Title: A family 8 glycoside hydrolase from Bacillus halodurans C-125 (BH2105) is a reducing end xylose-releasing exo-oligoxylanase Authors: Honda, Y. / Kitaoka, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dro.cif.gz | 100.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dro.ent.gz | 75.4 KB | Display | PDB format |
PDBx/mmJSON format | 2dro.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/2dro ftp://data.pdbj.org/pub/pdb/validation_reports/dr/2dro | HTTPS FTP |
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-Related structure data
Related structure data | 2drqC 2drrC 2drsC 3a3vC 1wu4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46116.855 Da / Num. of mol.: 1 / Mutation: K2E/D263C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: BH2105 / Plasmid: PET28B-BH2105 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD(DE3) References: UniProt: Q9KB30, oligosaccharide reducing-end xylanase | ||
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#2: Chemical | ChemComp-NI / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG4000, SODIUM ACETATE, GLYCEROL, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 7, 2005 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→61.546 Å / Num. all: 45145 / Num. obs: 44431 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 18.2 Å2 / Rsym value: 0.064 / Net I/σ(I): 27.45 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 4438 / Rsym value: 0.358 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1WU4 Resolution: 1.7→39.07 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.646 / SU ML: 0.056 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.094 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.68 Å2
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Refine analyze | Luzzati coordinate error obs: 0.1498 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→39.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.702→1.746 Å / Total num. of bins used: 20
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