[English] 日本語
Yorodumi- PDB-6g0b: Crystal Structure of a GH8 xylotriose complex from Teredinibacter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g0b | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of a GH8 xylotriose complex from Teredinibacter Turnerae | |||||||||
Components | Glycoside hydrolase family 8 domain protein | |||||||||
Keywords | HYDROLASE / Xylanse / complex / carbohydrate | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Teredinibacter turnerae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | |||||||||
Authors | Fowler, C.A. / Davies, G.J. / Walton, P.H. | |||||||||
Funding support | United Kingdom, 1items
| |||||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: Structure and function of a glycoside hydrolase family 8 endoxylanase from Teredinibacter turnerae. Authors: Fowler, C.A. / Hemsworth, G.R. / Cuskin, F. / Hart, S. / Turkenburg, J. / Gilbert, H.J. / Walton, P.H. / Davies, G.J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6g0b.cif.gz | 95.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6g0b.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 6g0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/6g0b ftp://data.pdbj.org/pub/pdb/validation_reports/g0/6g0b | HTTPS FTP |
---|
-Related structure data
Related structure data | 6g00SC 6g09C 6g0nC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 45112.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Teredinibacter turnerae (strain ATCC 39867 / T7901) (bacteria) Strain: ATCC 39867 / T7901 / Gene: TERTU_4506 / Production host: Escherichia coli (E. coli) References: UniProt: C5BJ89, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds |
---|---|
#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylotriose |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.54 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M sodium acetate, pH 5, 0.2 M ammonium sulfate, 20% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→59.47 Å / Num. obs: 40092 / % possible obs: 100 % / Redundancy: 7.9 % / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.8→1.84 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: 6G00 Resolution: 1.8→59.47 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.647 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.582 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.8→59.47 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|