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- PDB-1wu5: Crystal structure of reducing-end-xylose releasing exo-oligoxylan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1wu5 | |||||||||
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Title | Crystal structure of reducing-end-xylose releasing exo-oligoxylanase complexed with xylose | |||||||||
![]() | xylanase Y | |||||||||
![]() | HYDROLASE / (alpla/alpha)6 barrel / glycoside hydrolase family 8 | |||||||||
Function / homology | ![]() oligosaccharide reducing-end xylanase / oligosaccharide reducing-end xylanase activity / xylan catabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Fushinobu, S. / Hidaka, M. / Honda, Y. / Wakagi, T. / Shoun, H. / Kitaoka, M. | |||||||||
![]() | ![]() 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. #1: ![]() Title: Crystallization and preliminary X-ray analysis of reducing-end-xylose releasing exo-oligoxylanase (Rex) form Bacillus halodurans C-125 Authors: Honda, Y. / Fushinobu, S. / Hidaka, M. / Wakagi, T. / Shoun, H. / Kitaoka, M. #2: 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.9 KB | Display | ![]() |
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PDB format | ![]() | 72.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.1 KB | Display | ![]() |
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Full document | ![]() | 457.5 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wu4C ![]() 1wu6C ![]() 1h14S C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Details | The biological assembly is monomer in the asymmetric unit. |
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Components
#1: Protein | Mass: 46128.801 Da / Num. of mol.: 1 / Mutation: K2E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9KB30, oligosaccharide reducing-end xylanase |
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#2: Sugar | ChemComp-XYP / |
#3: Chemical | ChemComp-NI / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.3 % |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2004 |
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: 2.2→62.86 Å / Num. all: 20312 / Num. obs: 20272 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.7 Å2 / Rsym value: 0.084 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Mean I/σ(I) obs: 6.4 / Rsym value: 0.244 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1H14 Resolution: 2.2→44.88 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1724118.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.8661 Å2 / ksol: 0.368787 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→44.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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