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Yorodumi- PDB-3c7g: Crystal structure of a glycoside hydrolase family 43 arabinoxylan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c7g | |||||||||
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Title | Crystal structure of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase from Bacillus subtilis in complex with xylotetraose. | |||||||||
Components | Endo-1,4-beta-xylanase | |||||||||
Keywords | HYDROLASE / 5-bladed beta-propeller fold / beta-sandwich / Xylan degradation | |||||||||
Function / homology | Function and homology information 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 | Bacillus subtilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | |||||||||
Authors | Vandermarliere, E. / Bourgois, T.M. / Winn, M.D. / Van Campenhout, S. / Volckaert, G. / Strelkov, S.V. / Delcour, J.A. / Rabijns, A. / Courtin, C.M. | |||||||||
Citation | Journal: Biochem.J. / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c7g.cif.gz | 119.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c7g.ent.gz | 88.9 KB | Display | PDB format |
PDBx/mmJSON format | 3c7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/3c7g ftp://data.pdbj.org/pub/pdb/validation_reports/c7/3c7g | HTTPS FTP |
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-Related structure data
Related structure data | 3c7eC 3c7fC 3c7hC 3c7oC 1gyhS 1w9tS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 51763.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: xynD / Production host: Escherichia coli (E. coli) References: UniProt: Q45071, non-reducing end alpha-L-arabinofuranosidase |
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#2: 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 , 4 types, 450 molecules
#3: Chemical | ChemComp-CA / | ||||
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#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.25 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 4.0 M Na formate , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.0322 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0322 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→50 Å / Num. obs: 33537 / % possible obs: 97 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.046 / Rsym value: 4.6 |
Reflection shell | Resolution: 2.02→2.09 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 8 / Num. unique all: 1596 / Rsym value: 13.7 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entries 1gyh, 1w9t Resolution: 2.02→31.96 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.862 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.142 / 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: 13.734 Å2
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Refinement step | Cycle: LAST / Resolution: 2.02→31.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.069 Å / Total num. of bins used: 20
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