+Open data
-Basic information
Entry | Database: PDB / ID: 6g00 | ||||||
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Title | Crystal Structure of a GH8 xylanase from Teredinibacter turnerae | ||||||
Components | Glycoside hydrolase family 8 domain protein | ||||||
Keywords | HYDROLASE / Xylanse / native / carbohydrate | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Teredinibacter turnerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Fowler, C.A. / Davies, G.J. / Walton, P.H. | ||||||
Funding support | United Kingdom, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g00.cif.gz | 99.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g00.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 6g00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g00_validation.pdf.gz | 425.7 KB | Display | wwPDB validaton report |
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Full document | 6g00_full_validation.pdf.gz | 425.8 KB | Display | |
Data in XML | 6g00_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 6g00_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/6g00 ftp://data.pdbj.org/pub/pdb/validation_reports/g0/6g00 | HTTPS FTP |
-Related structure data
Related structure data | 6g09C 6g0bC 6g0nC 1wu4S 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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1 |
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Unit cell |
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-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) Gene: TERTU_4506 / Plasmid: pET-28 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: C5BJ89, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds | ||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.7 % |
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Crystal grow | Temperature: 291.2 K / Method: vapor diffusion, hanging drop / pH: 5 Details: sodium acetate (0.1M, pH 5.0), NaCl (0.2 M), polyethylene glycol 6000 16%. PH range: 4.6-5.2 / Temp details: temperature controlled room |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 1, 2016 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→51 Å / Num. obs: 80610 / % possible obs: 99.4 % / Redundancy: 4.3 % / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.4→1.42 Å |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WU4 Resolution: 1.4→56.97 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.017 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.305 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→56.97 Å
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Refine LS restraints |
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