+Open data
-Basic information
Entry | Database: PDB / ID: 2vuj | ||||||
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Title | Environmentally isolated GH11 xylanase | ||||||
Components | GH11 XYLANASE | ||||||
Keywords | HYDROLASE / GH11 / XYLANASE / GLYCOSIDASE | ||||||
Function / homology | Glycoside hydrolase family 11/12, catalytic domain / Jelly Rolls / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Dumon, C. / Varvak, A. / Wall, M.A. / Flint, J.E. / Lewis, R.J. / Lakey, J.H. / Luginbuhl, P. / Healey, S. / Todaro, T. / DeSantis, G. ...Dumon, C. / Varvak, A. / Wall, M.A. / Flint, J.E. / Lewis, R.J. / Lakey, J.H. / Luginbuhl, P. / Healey, S. / Todaro, T. / DeSantis, G. / Sun, M. / Parra-Gessert, L. / Tan, X. / Weiner, D.P. / Gilbert, H.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Engineering Hyperthermostability Into a Gh11 Xylanase is Mediated by Subtle Changes to Protein Structure. Authors: Dumon, C. / Varvak, A. / Wall, M.A. / Flint, J.E. / Lewis, R.J. / Lakey, J.H. / Morland, C. / Luginbuhl, P. / Healey, S. / Todaro, T. / Desantis, G. / Sun, M. / Parra-Gessert, L. / Tan, X. / ...Authors: Dumon, C. / Varvak, A. / Wall, M.A. / Flint, J.E. / Lewis, R.J. / Lakey, J.H. / Morland, C. / Luginbuhl, P. / Healey, S. / Todaro, T. / Desantis, G. / Sun, M. / Parra-Gessert, L. / Tan, X. / Weiner, D.P. / Gilbert, H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vuj.cif.gz | 59.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vuj.ent.gz | 41.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vuj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vuj_validation.pdf.gz | 440.4 KB | Display | wwPDB validaton report |
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Full document | 2vuj_full_validation.pdf.gz | 441.1 KB | Display | |
Data in XML | 2vuj_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 2vuj_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vu/2vuj ftp://data.pdbj.org/pub/pdb/validation_reports/vu/2vuj | HTTPS FTP |
-Related structure data
Related structure data | 2vulC 1xnbS 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
#1: Protein | Mass: 23545.732 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PSE420-CHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: endo-1,4-beta-xylanase |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Sequence details | CATALYTIC DOMAIN RESIDUES 1-218 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33 % / Description: NONE |
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Crystal grow | Temperature: 293 K / pH: 9 / Details: 12% (W/V) PEG 8000, 0.1 M TRIS/HCL (PH 9) AT 20 C |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Feb 24, 2005 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→24.2 Å / Num. obs: 16599 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.1 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XNB Resolution: 1.8→48.45 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.903 / SU B: 3.206 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.149 / 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: 15.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→48.45 Å
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Refine LS restraints |
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