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- PDB-5zkz: Crystal Structures of Mutant Endo-beta-1,4-xylanase II(Y77F) Comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zkz | |||||||||
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Title | Crystal Structures of Mutant Endo-beta-1,4-xylanase II(Y77F) Complexed with Xylotriose | |||||||||
![]() | Endo-1,4-beta-xylanase 2![]() | |||||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhang, X. / Wan, Q. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structures of Endo-beta-1,4-xylanase II Authors: Wan, Q. / Zhang, X. #1: ![]() 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. #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. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.3 KB | Display | ![]() |
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PDB format | ![]() | 66.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5zh0C ![]() 5ziiC ![]() 5ziwC ![]() 2dfcS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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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: 20711.338 Da / Num. of mol.: 1 / Mutation: Y77F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 56765 / BCRC 32924 / NRRL 11460 / Rut C-30 / Gene: xyn2, M419DRAFT_124931 / Production host: ![]() ![]() ![]() ![]() | ||
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#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylotriose | ||
#3: Chemical | ChemComp-GOL / ![]() | ||
#4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.34 % |
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Crystal grow![]() | Temperature: 291 K / Method: evaporation / pH: 6 / Details: 20% PEG 8000, 0.2M NaI, 0.1M MES |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.3→45.083 Å / Num. obs: 50491 / % possible obs: 99.52 % / Redundancy: 5.8 % / Biso Wilson estimate: 12.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0319 / Net I/σ(I): 13.99 |
Reflection shell | Resolution: 1.3→1.346 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.2865 / Mean I/σ(I) obs: 2.51 / Num. unique obs: 4934 / CC1/2: 0.803 / % possible all: 98.62 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2DFC Resolution: 1.3→45.083 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.07 / 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: 55.93 Å2 / Biso mean: 16.6966 Å2 / Biso min: 7.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3→45.083 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18
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