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- PDB-3c7e: Crystal structure of a glycoside hydrolase family 43 arabinoxylan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3c7e | ||||||
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Title | Crystal structure of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase from Bacillus subtilis. | ||||||
![]() | Endo-1,4-beta-xylanase | ||||||
![]() | HYDROLASE / 5-bladed beta-propeller fold / beta-sandwich / Xylan degradation | ||||||
Function / homology | ![]() non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / xylan catabolic process / carbohydrate binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vandermarliere, E. / Bourgois, T.M. / Winn, M.D. / Van Campenhout, S. / Volckaert, G. / Strelkov, S.V. / Delcour, J.A. / Rabijns, A. / Courtin, C.M. | ||||||
![]() | ![]() Title: Structural analysis of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase in complex with xylotetraose reveals a different binding mechanism compared with other members of the same family. Authors: Vandermarliere, E. / Bourgois, T.M. / Winn, M.D. / van Campenhout, S. / Volckaert, G. / Delcour, J.A. / Strelkov, S.V. / 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 | ![]() | 112.2 KB | Display | ![]() |
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PDB format | ![]() | 83.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.3 KB | Display | ![]() |
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Full document | ![]() | 440.5 KB | Display | |
Data in XML | ![]() | 21.9 KB | Display | |
Data in CIF | ![]() | 32.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3c7fC ![]() 3c7gC ![]() 3c7hC ![]() 3c7oC ![]() 1gyhS ![]() 1w9tS C: citing same article ( S: Starting model for refinement |
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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
#1: Protein | Mass: 51676.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q45071, non-reducing end alpha-L-arabinofuranosidase | ||||
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#2: Chemical | ChemComp-CA / | ||||
#3: Chemical | #4: Chemical | ChemComp-FMT / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.85 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 4.0 M Na formate, 30% sucrose, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 35773 / % possible obs: 96.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.102 / Rsym value: 10.2 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 3.9 / Num. unique all: 4966 / Rsym value: 33.3 / % possible all: 93.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entries 1w9t, 1gyh Resolution: 2→28.61 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.434 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.151 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.75 Å2
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Refinement step | Cycle: LAST / Resolution: 2→28.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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