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Yorodumi- PDB-7wrr: X-ray structure of Thermus thermophilus HB8 transketorase in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wrr | ||||||
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Title | X-ray structure of Thermus thermophilus HB8 transketorase in complex with TPP and MES | ||||||
Components | Transketolase | ||||||
Keywords | TRANSFERASE / transketolase / complex / TPP | ||||||
Function / homology | Function and homology information transketolase / transketolase activity / pentose-phosphate shunt / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Kamitori, S. / Yoshihara, A. | ||||||
Funding support | 1items
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Citation | Journal: Appl.Microbiol.Biotechnol. / Year: 2023 Title: Structural and biochemical characterizations of Thermus thermophilus HB8 transketolase producing a heptulose. Authors: Yoshihara, A. / Takamatsu, Y. / Mochizuki, S. / Yoshida, H. / Masui, R. / Izumori, K. / Kamitori, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wrr.cif.gz | 528.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wrr.ent.gz | 416.5 KB | Display | PDB format |
PDBx/mmJSON format | 7wrr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wrr_validation.pdf.gz | 4.8 MB | Display | wwPDB validaton report |
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Full document | 7wrr_full_validation.pdf.gz | 4.9 MB | Display | |
Data in XML | 7wrr_validation.xml.gz | 91.7 KB | Display | |
Data in CIF | 7wrr_validation.cif.gz | 128.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/7wrr ftp://data.pdbj.org/pub/pdb/validation_reports/wr/7wrr | HTTPS FTP |
-Related structure data
Related structure data | 7wrtC 2e6kS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 74230.727 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA0108 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SM35, transketolase #2: Chemical | ChemComp-TPP / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-MES / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.42 Å3/Da / Density % sol: 49.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 100mM imidazole/MES buffer pH 6.5, 20%(v/v) ethylene glycol, 10%(w/v) PEG 8000, 24mM of D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→46.67 Å / Num. obs: 175041 / % possible obs: 97.7 % / Redundancy: 3.5 % / CC1/2: 0.997 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.01→2.06 Å / Num. unique obs: 12801 / CC1/2: 0.732 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2E6K Resolution: 2.01→46.67 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.287 / SU ML: 0.139 / Cross valid method: FREE R-VALUE / ESU R: 0.205 / ESU R Free: 0.167 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: 43.074 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→46.67 Å
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Refine LS restraints |
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LS refinement shell |
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