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Yorodumi- PDB-3vzj: Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vzj | ||||||
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Title | Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) E172H mutant | ||||||
Components | Endo-1,4-beta-xylanaseXylanase | ||||||
Keywords | HYDROLASE / xylanase / GH-11 glycoside hydrolase | ||||||
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: 2.406 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 | 3vzj.cif.gz | 151.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vzj.ent.gz | 121 KB | Display | PDB format |
PDBx/mmJSON format | 3vzj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/3vzj ftp://data.pdbj.org/pub/pdb/validation_reports/vz/3vzj | HTTPS FTP |
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-Related structure data
Related structure data | 3vzkC 3vzlC 3vzmC 3vznC 3vzoC 1hv1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 20418.037 Da / Num. of mol.: 4 / Mutation: E172H 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 #2: Chemical | #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: 2.02 Å3/Da / Density % sol: 39.26 % |
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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: Jun 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: 2.4→38.167 Å / Num. all: 35327 / Num. obs: 31471 / % possible obs: 91 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 34 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HV1 Resolution: 2.406→38.167 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6371 / SU ML: 0.59 / σ(F): 1.41 / Phase error: 40.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.951 Å2 / ksol: 0.366 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.24 Å2 / Biso mean: 30.8582 Å2 / Biso min: 11.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.406→38.167 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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