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- PDB-3w25: The high-resolution crystal structure of TsXylA, intracellular xy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3w25 | |||||||||
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Title | The high-resolution crystal structure of TsXylA, intracellular xylanase from /Thermoanaerobacterium saccharolyticum JW/SL-YS485/: the complex of the E146A mutant with xylobiose | |||||||||
![]() | Glycoside hydrolase family 10 | |||||||||
![]() | HYDROLASE / glycoside hydrolase / xylanase / thermophilic / xylobiose | |||||||||
Function / homology | ![]() endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / polysaccharide catabolic process / carbohydrate binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Han, X. / Gao, J. / Shang, N. / Huang, C.-H. / Ko, T.-P. / Zhu, Z. / Wiegel, J. / Shao, W. / Guo, R.-T. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.1 KB | Display | ![]() |
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PDB format | ![]() | 70.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3w24SC ![]() 3w26C ![]() 3w27C ![]() 3w28C ![]() 3w29C ![]() 3w2b S: Starting model for refinement C: citing same article ( |
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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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Components
#1: Protein | Mass: 38005.020 Da / Num. of mol.: 1 / Fragment: UNP residues 349-684 / Mutation: E146A,P326L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: JW/SL-YS485 / Gene: Tsac_1459 / Plasmid: pET46 / Production host: ![]() ![]() |
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#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylobiose |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.93 % |
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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: ![]() ![]() ![]() |
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 | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→25 Å / Num. all: 98337 / Num. obs: 98337 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.32→1.37 Å / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.068 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3W24 Resolution: 1.32→25 Å / Occupancy max: 1 / Occupancy min: 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 45.9114 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 53.68 Å2 / Biso mean: 15.4165 Å2 / Biso min: 4.38 Å2
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Refinement step | Cycle: LAST / Resolution: 1.32→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.32→1.37 Å |