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Yorodumi- PDB-4n6f: Crystal structure of Amycolatopsis orientalis BexX complexed with G6P -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n6f | ||||||
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Title | Crystal structure of Amycolatopsis orientalis BexX complexed with G6P | ||||||
Components | Putative thiosugar synthase | ||||||
Keywords | LYASE / Tim barrel / BexX / thiosugar synthase | ||||||
Function / homology | Function and homology information thiazole synthase activity / thiazole synthase / thiamine diphosphate biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Amycolatopsis orientalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Zhang, X. / Zhang, Y. / Kinsland, C. / Sasaki, E. / Sun, H.G. / Lu, M.J. / Liu, T. / Ou, A. / Li, J. / Chen, Y. ...Zhang, X. / Zhang, Y. / Kinsland, C. / Sasaki, E. / Sun, H.G. / Lu, M.J. / Liu, T. / Ou, A. / Li, J. / Chen, Y. / Liu, H. / Ealick, S.E. | ||||||
Citation | Journal: Nature / Year: 2014 Title: Co-opting sulphur-carrier proteins from primary metabolic pathways for 2-thiosugar biosynthesis. Authors: Sasaki, E. / Zhang, X. / Sun, H.G. / Lu, M.Y. / Liu, T.L. / Ou, A. / Li, J.Y. / Chen, Y.H. / Ealick, S.E. / Liu, H.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n6f.cif.gz | 100.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n6f.ent.gz | 81.6 KB | Display | PDB format |
PDBx/mmJSON format | 4n6f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n6f_validation.pdf.gz | 1013.3 KB | Display | wwPDB validaton report |
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Full document | 4n6f_full_validation.pdf.gz | 1015.1 KB | Display | |
Data in XML | 4n6f_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 4n6f_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/4n6f ftp://data.pdbj.org/pub/pdb/validation_reports/n6/4n6f | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27126.107 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amycolatopsis orientalis (bacteria) / Strain: subsp. vinearia / Gene: bexX / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D7RFL7 #2: Chemical | ChemComp-CA / #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.79 Å3/Da / Density % sol: 55.85 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 40% (v/v) PEG300, 0.1 M sodium cacodylate/HCl, pH 6.5, 0.2 M calcium acetate, vapor diffusion, hanging drop, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9767 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 24, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9767 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→50 Å / Num. obs: 29855 / % possible obs: 100 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.064 / Χ2: 0.883 / Net I/σ(I): 12.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→46.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.185 / 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 max: 82.16 Å2 / Biso mean: 39.0295 Å2 / Biso min: 19.86 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→46.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
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