[English] 日本語
Yorodumi- PDB-7dfo: Crystal structure of glycoside hydrolase family 11 beta-xylanase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dfo | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces olivaceoviridis E-86 in complex with 4-O-methyl-alpha-D-glucuronopyranosyl 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7dfo.cif.gz | 373.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7dfo.ent.gz | 295.7 KB | Display | PDB format |
PDBx/mmJSON format | 7dfo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dfo_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7dfo_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7dfo_validation.xml.gz | 68.5 KB | Display | |
Data in CIF | 7dfo_validation.cif.gz | 99.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/7dfo ftp://data.pdbj.org/pub/pdb/validation_reports/df/7dfo | HTTPS FTP |
-Related structure data
Related structure data | 7dfmSC 7dfnC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
-Components
-Protein , 1 types, 9 molecules ABCDEFGHI
#1: Protein | Mass: 22537.367 Da / Num. of mol.: 9 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 |
---|
-Sugars , 4 types, 8 molecules
#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose #3: Polysaccharide | #4: Polysaccharide | 4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)- ...4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose | #5: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose | |
---|
-Non-polymers , 3 types, 904 molecules
#6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-NA / #8: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.43 % / Description: rod |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→100 Å / Num. obs: 110677 / % possible obs: 99.3 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.165 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.839 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 11151 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DFM Resolution: 2→47.061 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.858 / SU ML: 0.131 / Cross valid method: FREE R-VALUE / ESU R: 0.19 / ESU R Free: 0.166 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 30.941 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→47.061 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|