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Yorodumi- PDB-7dfn: Crystal structure of glycoside hydrolase family 11 beta-xylanase ... -
+Open data
-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 | ||||||
Components | Endo-1,4-beta-xylanase | ||||||
Keywords | HYDROLASE / glycoside hydrolase family 11 | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | ||||||
Biological species | Streptomyces olivaceoviridis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Fujimoto, Z. / Kishine, N. / Kaneko, S. | ||||||
Citation | Journal: Appl.Microbiol.Biotechnol. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dfn.cif.gz | 177.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dfn.ent.gz | 136.2 KB | Display | PDB format |
PDBx/mmJSON format | 7dfn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dfn_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7dfn_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7dfn_validation.xml.gz | 33.9 KB | Display | |
Data in CIF | 7dfn_validation.cif.gz | 50.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/7dfn ftp://data.pdbj.org/pub/pdb/validation_reports/df/7dfn | HTTPS FTP |
-Related structure data
Related structure data | 7dfmSC 7dfoC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) Streptomyces olivaceoviridis (bacteria) Strain: E-86 / Gene: gxyn1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A7G1MBT0*PLUS, endo-1,4-beta-xylanase #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
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: 1 Å / Relative weight: 1 |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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