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- PDB-2qz3: Crystal structure of a glycoside hydrolase family 11 xylanase fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2qz3 | |||||||||
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Title | Crystal structure of a glycoside hydrolase family 11 xylanase from Bacillus subtilis in complex with xylotetraose | |||||||||
![]() | Endo-1,4-beta-xylanase A | |||||||||
![]() | HYDROLASE / glycoside hydrolase / xylanase / Glycosidase / Xylan degradation | |||||||||
Function / homology | ![]() endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Vandermarliere, E. / Bourgois, T.M. / Strelkov, S.V. / Delcour, J.A. / Courtin, C.M. / Rabijns, A. | |||||||||
![]() | ![]() Title: Crystallographic analysis shows substrate binding at the -3 to +1 active-site subsites and at the surface of glycoside hydrolase family 11 endo-1,4-beta-xylanases. Authors: Vandermarliere, E. / Bourgois, T.M. / Rombouts, S. / Van Campenhout, S. / Volckaert, G. / Strelkov, S.V. / Delcour, J.A. / Rabijns, A. / Courtin, C.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.1 KB | Display | ![]() |
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PDB format | ![]() | 71.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2qz2C ![]() 2z79C ![]() 1bcxS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20336.943 Da / Num. of mol.: 2 / Mutation: E172A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylotriose #3: Chemical | ChemComp-ACY / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M ammonium sulphate, 0.1M Tris-HCl pH 8.5, 30% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 12, 2006 |
Radiation | Monochromator: Fixed exit double crystal Si [111], horizontally focussing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 31423 / Num. obs: 30942 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.4 / Rsym value: 0.044 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.8→1.83 Å / Mean I/σ(I) obs: 11.5 / Num. unique all: 1547 / Rsym value: 0.089 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BCX Resolution: 1.8→19.91 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.029 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.35 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.802→1.849 Å / Total num. of bins used: 20
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