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- PDB-7ayp: Structure of a GH11 domain refined from the X-ray diffraction dat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ayp | ||||||
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Title | Structure of a GH11 domain refined from the X-ray diffraction data of a GH11-CBM36-1 crystal. | ||||||
![]() | Endo-1,4-beta-xylanase | ||||||
![]() | HYDROLASE / Multidomain protein / carbohydrate binding domains / GH11 / interdomain interactions / carbohydrate esterases / Isothermal titration calorimetry | ||||||
Function / homology | ![]() hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Anye, V. / Schubert, W.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and biophysical characterization of the multidomain xylanase Xyl. Authors: Anye, V. / Kruger, R.F. / Schubert, W.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.7 KB | Display | ![]() |
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PDB format | ![]() | 41.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 414.8 KB | Display | ![]() |
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Full document | ![]() | 414.9 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 14.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ax7C ![]() 7ay3C ![]() 7zszC ![]() 2dcjS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 46589.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GH11-CBM36-1 Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.48 % |
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Crystal grow | Temperature: 293.16 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: Na acetate, (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.65 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→93.69 Å / Num. obs: 65364 / % possible obs: 99.9 % / Redundancy: 1 % / Biso Wilson estimate: 14.6903258564 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.81 |
Reflection shell | Resolution: 1.47→3.9 Å / Num. unique obs: 3225 / CC1/2: 0.814 / % possible all: 99 |
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Processing
Software | Name: PHENIX / Version: 1.12_2829 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 2DCJ Resolution: 1.70001286876→54.108 Å / SU ML: 0.143195300177 / Cross valid method: FREE R-VALUE / σ(F): 1.33571280734 / Phase error: 17.930989269 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.9406706224 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.70001286876→54.108 Å
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Refine LS restraints |
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LS refinement shell |
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