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Yorodumi- PDB-2z79: High resolution crystal structure of a glycoside hydrolase family... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z79 | ||||||
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Title | High resolution crystal structure of a glycoside hydrolase family 11 xylanase of Bacillus subtilis | ||||||
Components | Endo-1,4-beta-xylanase A | ||||||
Keywords | HYDROLASE / glycoside hydrolase / xylanase / Glycosidase / Xylan degradation | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Vandermarliere, E. / Bourgois, T.M. / Strelkov, S.V. / Delcour, J.A. / Courtin, C.M. / Rabijns, A. | ||||||
Citation | Journal: Biochem.J. / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z79.cif.gz | 165 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z79.ent.gz | 130.5 KB | Display | PDB format |
PDBx/mmJSON format | 2z79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/2z79 ftp://data.pdbj.org/pub/pdb/validation_reports/z7/2z79 | HTTPS FTP |
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-Related structure data
Related structure data | 2qz2C 2qz3C 1bcxS 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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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.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P18429, endo-1,4-beta-xylanase #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M imidazole pH 6.5, 1.0M sodium acetate trihydrate, 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: 0.9918 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 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: 0.9918 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→30 Å / Num. all: 73641 / Num. obs: 70534 / % possible obs: 89.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.4 / Rsym value: 0.086 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.3→1.32 Å / Mean I/σ(I) obs: 5.7 / Num. unique all: 3109 / Rsym value: 0.165 / % possible all: 80.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BCX Resolution: 1.3→22.83 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.449 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.054 / 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: 12.84 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→22.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
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