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- PDB-8c48: Crystal structure of Thermothelomyces thermophila GH30 (double mu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8c48 | ||||||||||||
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Title | Crystal structure of Thermothelomyces thermophila GH30 (double mutant EE) in complex with xylopentaose | ||||||||||||
![]() | GH30 family xylanase | ||||||||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Dimarogona, M. / Pentari, C. / Kosinas, C. / Topakas, E. | ||||||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: Structural and molecular insights into a bifunctional glycoside hydrolase 30 xylanase specific to glucuronoxylan. Authors: Pentari, C. / Kosinas, C. / Nikolaivits, E. / Dimarogona, M. / Topakas, E. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 398.6 KB | Display | ![]() |
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PDB format | ![]() | 326 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8cbcC ![]() 8p67C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 51728.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: G2Q1N4, ![]() |
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-Sugars , 5 types, 5 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose- ...beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose![]() Source method: isolated from a genetically manipulated source |
#5: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose![]() Source method: isolated from a genetically manipulated source |
#6: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose![]() Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 794 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/F.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/F.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ![]() #8: Chemical | ChemComp-F / | ![]() #9: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 38.98 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Sodium fluoride, Sodium bromide, Sodium iodide, Sodium HEPES, MOPS,PEG 500 MME, PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 30, 2022 |
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.34→45.98 Å / Num. obs: 159903 / % possible obs: 98.9 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.34→1.36 Å / Redundancy: 6.9 % / Num. unique obs: 56330 / CC1/2: 0.394 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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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: 23.789 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→45.98 Å
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Refine LS restraints |
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