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Open data
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Basic information
Entry | Database: PDB / ID: 4xqd | |||||||||
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Title | X-ray structure analysis of xylanase-WT at pH4.0 | |||||||||
![]() | Endo-1,4-beta-xylanase 2![]() | |||||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Wan, Q. / Park, J.M. / Riccardi, D.M. / Hanson, L.B. / Fisher, Z. / Smith, J.C. / Ostermann, A. / Schrader, T. / Graham, D.E. / Coates, L. ...Wan, Q. / Park, J.M. / Riccardi, D.M. / Hanson, L.B. / Fisher, Z. / Smith, J.C. / Ostermann, A. / Schrader, T. / Graham, D.E. / Coates, L. / Langan, P. / Kovalevsky, A.Y. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography. Authors: Wan, Q. / Parks, J.M. / Hanson, B.L. / Fisher, S.Z. / Ostermann, A. / Schrader, T.E. / Graham, D.E. / Coates, L. / Langan, P. / Kovalevsky, A. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Preliminary joint X-ray and neutron protein crystallographic studies of endoxylanase II from the fungus Trichoderma longibrachiatum. Authors: Kovalevsky, A.Y. / Hanson, B.L. / Seaver, S. / Fisher, S.Z. / Mustyakimov, M. / Langan, P. #2: ![]() Title: X-ray crystallographic studies of family 11 xylanase Michaelis and product complexes: implications for the catalytic mechanism. Authors: Wan, Q. / Zhang, Q. / Hamilton-Brehm, S. / Weiss, K. / Mustyakimov, M. / Coates, L. / Langan, P. / Graham, D. / Kovalevsky, A. #3: Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Heterologous expression, purification, crystallization and preliminary X-ray analysis of Trichoderma reesei xylanase II and four variants. Authors: Wan, Q. / Kovalevsky, A. / Zhang, Q. / Hamilton-Brehm, S. / Upton, R. / Weiss, K.L. / Mustyakimov, M. / Graham, D. / Coates, L. / Langan, 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 | ![]() | 98.4 KB | Display | ![]() |
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PDB format | ![]() | 73.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4s2dC ![]() 4s2fC ![]() 4s2gC ![]() 4s2hC ![]() 4xpvC ![]() 4xq4C ![]() 4xqwC ![]() 2dfbS 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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Details | biological unit is the same as asym. |
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Components
#1: Protein | ![]() Mass: 20727.338 Da / Num. of mol.: 2 / Fragment: substrate-binding groove, jelly roll Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-IOD / ![]() #3: Chemical | ChemComp-TRS / | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.76 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 20% PEG8000, 0.2 M NaI, 0.1 M NaOAc at pH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 12, 2013 / Details: Mirrors |
Radiation | Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.5→20 Å / Num. obs: 56145 / % possible obs: 91.2 % / Redundancy: 2.3 % / Rsym value: 0.098 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.1 / % possible all: 88.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2DFB Resolution: 1.5→19.956 Å / FOM work R set: 0.8158 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.38 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.7 Å2 / Biso mean: 19.67 Å2 / Biso min: 3.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→19.956 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: 20
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