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Yorodumi- PDB-3vzo: Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vzo | |||||||||
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Title | Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35H mutant with Glu78 covalently bonded to 2-deoxy-2-fluoro-xylobiose | |||||||||
Components | Endo-1,4-beta-xylanaseXylanase | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / xylanase / GH-11 glycoside hydrolase / glycosyl-enzyme intermediate / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
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 circulans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | |||||||||
Authors | Ludwiczek, M.L. / D'Angelo, I. / Yalloway, G.N. / Okon, M. / Nielsen, J.E. / Strynadka, N.C. / Withers, S.G. / McIntosh, L.P. | |||||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Strategies for modulating the pH-dependent activity of a family 11 glycoside hydrolase Authors: Ludwiczek, M.L. / D'Angelo, I. / Yalloway, G.N. / Brockerman, J.A. / Okon, M. / Nielsen, J.E. / Strynadka, N.C. / Withers, S.G. / McIntosh, L.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vzo.cif.gz | 57.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vzo.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 3vzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/3vzo ftp://data.pdbj.org/pub/pdb/validation_reports/vz/3vzo | HTTPS FTP |
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-Related structure data
Related structure data | 3vzjC 3vzkC 3vzlC 3vzmC 3vznC 1bvvS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 20433.049 Da / Num. of mol.: 1 / Mutation: N35H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus circulans (bacteria) / Gene: xlnA / Production host: Escherichia coli (E. coli) / References: UniProt: P09850, endo-1,4-beta-xylanase | ||
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#2: Polysaccharide | beta-D-xylopyranose-(1-4)-1,5-anhydro-2-deoxy-2-fluoro-D-xylitol Source method: isolated from a genetically manipulated source | ||
#3: Chemical | #4: 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: 2.04 Å3/Da / Density % sol: 39.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→60 Å / Num. all: 25987 / Num. obs: 23696 / % possible obs: 91 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BVV Resolution: 1.73→43.4 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.068 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.116 / 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: 17.629 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→43.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.733→1.778 Å / Total num. of bins used: 20
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