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- PDB-3vzm: Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vzm | |||||||||
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Title | Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) E172H mutant with Glu78 covalently bonded to 2-deoxy-2-fluoro-xylobiose | |||||||||
![]() | Endo-1,4-beta-xylanase | |||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / xylanase / GH-11 glycoside hydrolase / glycosyl-enzyme intermediate / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | ![]() endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Ludwiczek, M.L. / D'Angelo, I. / Yalloway, G.N. / Okon, M. / Nielsen, J.E. / Strynadka, N.C. / Withers, S.G. / McIntosh, L.P. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.1 KB | Display | ![]() |
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PDB format | ![]() | 37.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 706.7 KB | Display | ![]() |
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Full document | ![]() | 708.3 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 16 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vzjC ![]() 3vzkC ![]() 3vzlC ![]() 3vznC ![]() 3vzoC ![]() 1hv1S 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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Unit cell |
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Components
#1: Protein | Mass: 20418.037 Da / Num. of mol.: 1 / Mutation: E172H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.25 % |
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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: ![]() |
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: 1.67→60 Å / Num. all: 54287 / Num. obs: 49715 / % possible obs: 92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1HV1 Resolution: 1.86→22.43 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.181 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.183 / 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: 23.133 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→22.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.856→1.903 Å / Total num. of bins used: 20
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