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Yorodumi- PDB-4hu8: Crystal Structure of a Bacterial Ig-like Domain Containing GH10 X... -
+Open data
-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 | ||||||
Components | GH10 Xylanase | ||||||
Keywords | HYDROLASE / (alpha/beta)8 barrel / Big2 / glycoside hydrolase / bacterial Ig-like domain | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | ||||||
Biological species | Globitermes brachycerastes (cockroach) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: Biotechnol.Bioeng. / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hu8.cif.gz | 743.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hu8.ent.gz | 613.7 KB | Display | PDB format |
PDBx/mmJSON format | 4hu8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/4hu8 ftp://data.pdbj.org/pub/pdb/validation_reports/hu/4hu8 | HTTPS FTP |
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-Related structure data
Related structure data | 1nq6S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
-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.) Globitermes brachycerastes (cockroach) / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: K7PDC1*PLUS, endo-1,4-beta-xylanase #2: Chemical | ChemComp-SO4 / #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: 2.64 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: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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