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Yorodumi- PDB-3w28: The high-resolution crystal structure of TsXylA, intracellular xy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w28 | |||||||||
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Title | The high-resolution crystal structure of TsXylA, intracellular xylanase from /Thermoanaerobacterium saccharolyticum JW/SL-YS485/: the complex of the E251A mutant with xylotriose | |||||||||
Components | Glycoside hydrolase family 10 | |||||||||
Keywords | HYDROLASE / glycoside hydrolase / xylanase / thermophilic / xylotriose | |||||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / polysaccharide catabolic process / carbohydrate binding Similarity search - Function | |||||||||
Biological species | Thermoanaerobacterium saccharolyticum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å | |||||||||
Authors | Han, X. / Gao, J. / Shang, N. / Huang, C.-H. / Ko, T.-P. / Zhu, Z. / Wiegel, J. / Shao, W. / Guo, R.-T. | |||||||||
Citation | Journal: Proteins / Year: 2013 Title: Structural and functional analyses of catalytic domain of GH10 xylanase from Thermoanaerobacterium saccharolyticum JW/SL-YS485 Authors: Han, X. / Gao, J. / Shang, N. / Huang, C.-H. / Ko, T.-P. / Chen, C.C. / Chan, H.C. / Cheng, Y.S. / Zhu, Z. / Wiegel, J. / Luo, W. / Guo, R.-T. / Ma, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w28.cif.gz | 96.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w28.ent.gz | 70.3 KB | Display | PDB format |
PDBx/mmJSON format | 3w28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w28_validation.pdf.gz | 690.4 KB | Display | wwPDB validaton report |
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Full document | 3w28_full_validation.pdf.gz | 693.3 KB | Display | |
Data in XML | 3w28_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 3w28_validation.cif.gz | 34.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/3w28 ftp://data.pdbj.org/pub/pdb/validation_reports/w2/3w28 | HTTPS FTP |
-Related structure data
Related structure data | 3w24SC 3w25C 3w26C 3w27C 3w29C 3w2b 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: 38005.020 Da / Num. of mol.: 1 / Fragment: UNP residues 349-684 / Mutation: E251A,P326L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacterium saccharolyticum (bacteria) Strain: JW/SL-YS485 / Gene: Tsac_1459 / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I3VVC1, endo-1,4-beta-xylanase |
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#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-xylopyranose Source method: isolated from a genetically manipulated source |
#3: 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: 2.75 Å3/Da / Density % sol: 55.32 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris, 25% PEG 6000, 0.8M LiCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.39→25 Å / Num. all: 84274 / Num. obs: 84274 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 1.39→1.44 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 3.8 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W24 Resolution: 1.39→25 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 41.3809 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 52.41 Å2 / Biso mean: 18.7548 Å2 / Biso min: 6.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.39→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.39→1.44 Å |