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- PDB-4hu8: Crystal Structure of a Bacterial Ig-like Domain Containing GH10 X... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hu8 | ||||||
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Title | Crystal Structure of a Bacterial Ig-like Domain Containing GH10 Xylanase from Termite Gut | ||||||
![]() | GH10 Xylanase | ||||||
![]() | HYDROLASE / (alpha/beta)8 barrel / Big2 / glycoside hydrolase / bacterial Ig-like domain | ||||||
Function / homology | ![]() endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Han, Q. / Liu, N. / Robinson, H. / Cao, L. / Qian, C. / Wang, Q. / Xie, L. / Ding, H. / Wang, Q. / Huang, Y. ...Han, Q. / Liu, N. / Robinson, H. / Cao, L. / Qian, C. / Wang, Q. / Xie, L. / Ding, H. / Wang, Q. / Huang, Y. / Li, J. / Zhou, Z. | ||||||
![]() | ![]() Title: Biochemical characterization and crystal structure of a GH10 xylanase from termite gut bacteria reveal a novel structural feature and significance of its bacterial Ig-like domain. Authors: Han, Q. / Liu, N. / Robinson, H. / Cao, L. / Qian, C. / Wang, Q. / Xie, L. / Ding, H. / Wang, Q. / Huang, Y. / Li, J. / Zhou, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 743.2 KB | Display | ![]() |
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PDB format | ![]() | 613.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 520.5 KB | Display | ![]() |
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Full document | ![]() | 556.6 KB | Display | |
Data in XML | ![]() | 143.2 KB | Display | |
Data in CIF | ![]() | 206.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nq6S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
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Components
#1: Protein | Mass: 51207.707 Da / Num. of mol.: 8 / Fragment: GH10 Xylanase catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.36 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2 M potassium sodium tartrate tetrahydrate, 0.1 M sodium citrate tribasic dihydrate, 2 M ammonium sulfate, 20% glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 280K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 6, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 293766 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 2 / % possible all: 96 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1nq6 Resolution: 2→49.08 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.894 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.467 Å2
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Refinement step | Cycle: LAST / Resolution: 2→49.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.999→2.05 Å / Total num. of bins used: 20
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