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Yorodumi- PDB-7dfm: Crystal structure of glycoside hydrolase family 11 beta-xylanase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dfm | ||||||
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Title | Crystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces olivaceoviridis E-86 | ||||||
Components | Endo-1,4-beta-xylanaseXylanase | ||||||
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: 2.4 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 | 7dfm.cif.gz | 164.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dfm.ent.gz | 125.7 KB | Display | PDB format |
PDBx/mmJSON format | 7dfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/7dfm ftp://data.pdbj.org/pub/pdb/validation_reports/df/7dfm | HTTPS FTP |
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-Related structure data
Related structure data | 7dfnC 7dfoC 1hixS 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
#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: soxB / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A7G1MBT0*PLUS, endo-1,4-beta-xylanase #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.11 Å3/Da / Density % sol: 41.77 % / 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: 2.4→100 Å / Num. obs: 30040 / % possible obs: 100 % / Redundancy: 19.3 % / Rmerge(I) obs: 0.225 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2952 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HIX Resolution: 2.4→49.409 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.141 / SU B: 8.897 / SU ML: 0.199 / Average fsc free: 0.906 / Average fsc work: 0.9307 / Cross valid method: THROUGHOUT / ESU R: 0.518 / ESU R Free: 0.278 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: 26.848 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→49.409 Å
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Refine LS restraints |
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LS refinement shell |
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