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Yorodumi- PDB-5gqd: Crystal structure of covalent glycosyl-enzyme intermediate of xyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gqd | |||||||||
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Title | Crystal structure of covalent glycosyl-enzyme intermediate of xylanase mutant (T82A, N127S, and E128H) from Streptomyces olivaceoviridis E-86 | |||||||||
Components | Beta-xylanaseXylanase | |||||||||
Keywords | HYDROLASE / xylanase / mutant / pNP-xylobioside / covalent glycosyl-enzyme intermediate | |||||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / polysaccharide catabolic process Similarity search - Function | |||||||||
Biological species | Streptomyces olivaceoviridis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Suzuki, R. / Fujimoto, Z. / Kaneko, S. / Kuno, A. | |||||||||
Citation | Journal: J.Appl.Glyosci. / Year: 2019 Title: Azidolysis by the Formation of Stable Ser-His Catalytic Dyad in a Glycoside Hydrolase Family 10 Xylanase Mutant Authors: Suzuki, R. / Fujimoto, Z. / Kaneko, S. / Hasegawa, T. / Kuno, A. #1: Journal: J. Biochem. / Year: 2009 Title: Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86 Authors: Suzuki, R. / Fujimoto, Z. / Ito, S. / Kawahara, S. / Kaneko, S. / Taira, K. / Hasegawa, T. / Kuno, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gqd.cif.gz | 199.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gqd.ent.gz | 154.6 KB | Display | PDB format |
PDBx/mmJSON format | 5gqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/5gqd ftp://data.pdbj.org/pub/pdb/validation_reports/gq/5gqd | HTTPS FTP |
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-Related structure data
Related structure data | 5gqeC 2d1zS 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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-Components
#1: Protein | Mass: 46743.207 Da / Num. of mol.: 2 / Mutation: T82A, N127S, E128H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces olivaceoviridis (bacteria) Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7SI98, endo-1,4-beta-xylanase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #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: 2.86 Å3/Da / Density % sol: 56.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: 25% ammonium sulfate 2% Mcllvaine buffer |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 5, 2005 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 94763 / % possible obs: 98.4 % / Redundancy: 7.3 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 32.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 6.1 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2D1Z Resolution: 1.8→40.09 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2814853.41 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 73.9289 Å2 / ksol: 0.400613 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→40.09 Å /
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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