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- PDB-7dfn: Crystal structure of glycoside hydrolase family 11 beta-xylanase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dfn | ||||||
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Title | Crystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces olivaceoviridis E-86 in complex with alpha-L-arabinofuranosyl xylotetraose | ||||||
![]() | Endo-1,4-beta-xylanase![]() | ||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fujimoto, Z. / Kishine, N. / Kaneko, S. | ||||||
![]() | ![]() Title: Structure-based substrate specificity analysis of GH11 xylanase from Streptomyces olivaceoviridis E-86. Authors: Fujimoto, Z. / Kishine, N. / Teramoto, K. / Tsutsui, S. / Kaneko, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177.8 KB | Display | ![]() |
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PDB format | ![]() | 136.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7dfmSC ![]() 7dfoC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 22537.367 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: GB LC578783 Source: (gene. exp.) ![]() ![]() Strain: E-86 / Gene: gxyn1 / Production host: ![]() ![]() ![]() References: UniProt: A0A7G1MBT0*PLUS, ![]() #2: Polysaccharide | ![]() #3: Chemical | ChemComp-CL / ![]() #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.98 % / Description: needle |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4 Details: 2.9 M sodium chloride, 0.1 M sodium citrate buffer pH 5.4 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→100 Å / Num. obs: 50743 / % possible obs: 99.8 % / Redundancy: 17.4 % / Rmerge(I) obs: 0.257 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 48052 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7DFM Resolution: 2→49.217 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.599 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / ESU R: 0.187 / ESU R Free: 0.159 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.721 Å2
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Refinement step | Cycle: LAST / Resolution: 2→49.217 Å
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Refine LS restraints |
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LS refinement shell |
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