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Yorodumi- PDB-1wu4: Crystal structure of reducing-end-xylose releasing exo-oligoxylanase -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wu4 | ||||||
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Title | Crystal structure of reducing-end-xylose releasing exo-oligoxylanase | ||||||
Components | xylanase Y | ||||||
Keywords | HYDROLASE / (alpla/alpha)6 barrel / glycoside hydrolase family 8 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Fushinobu, S. / Hidaka, M. / Honda, Y. / Wakagi, T. / Shoun, H. / Kitaoka, M. | ||||||
Citation | 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. #1: Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wu4.cif.gz | 103.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wu4.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 1wu4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wu4_validation.pdf.gz | 434.1 KB | Display | wwPDB validaton report |
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Full document | 1wu4_full_validation.pdf.gz | 436.3 KB | Display | |
Data in XML | 1wu4_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 1wu4_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/1wu4 ftp://data.pdbj.org/pub/pdb/validation_reports/wu/1wu4 | HTTPS FTP |
-Related structure data
Related structure data | 1wu5C 1wu6C 1h14S 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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Unit cell |
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Details | The biological assembly is monomer in the asymmetric unit. |
-Components
#1: Protein | Mass: 46128.801 Da / Num. of mol.: 1 / Mutation: K2E 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 | ChemComp-GOL / |
#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: 2.21 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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
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: 1.35→62.02 Å / Num. all: 88485 / Num. obs: 87069 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.7 Å2 / Rsym value: 0.053 / Net I/σ(I): 36 |
Reflection shell | Resolution: 1.35→1.4 Å / Mean I/σ(I) obs: 4.7 / Rsym value: 0.285 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H14 Resolution: 1.35→25.19 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1499592.9 / 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: 48.9171 Å2 / ksol: 0.367881 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.35→25.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.43 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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