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Yorodumi- PDB-5gtw: The N253R mutant structures of trehalose synthase from Deinococcu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gtw | ||||||
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Title | The N253R mutant structures of trehalose synthase from Deinococcus radiodurans display two different active-site conformations | ||||||
Components | Trehalose synthase | ||||||
Keywords | ISOMERASE / Trehalose synthase / Glycoside hydrolase family 13 | ||||||
Function / homology | Function and homology information maltose alpha-D-glucosyltransferase / maltose alpha-D-glucosyltransferase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans R1 (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å | ||||||
Authors | Chow, S.Y. / Wei, Y.J. / Liaw, S.H. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: To Be Published Title: The N253R mutant structures of trehalose synthase from Deinococcus radiodurans display two different active-site conformations Authors: Chow, S.Y. / Wei, Y.J. / Liaw, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gtw.cif.gz | 441.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gtw.ent.gz | 359.7 KB | Display | PDB format |
PDBx/mmJSON format | 5gtw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/5gtw ftp://data.pdbj.org/pub/pdb/validation_reports/gt/5gtw | HTTPS FTP |
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-Related structure data
Related structure data | 4tvuS S: Starting model for refinement |
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Similar structure data |
-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: 65030.938 Da / Num. of mol.: 4 / Mutation: R97W,N253R,T313I,I380V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant) Strain: R1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: I3NX86, maltose alpha-D-glucosyltransferase #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-MG / #4: Chemical | #5: 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: 2.5 Å3/Da / Density % sol: 50.79 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 8% PEG 4000, 0.2M sodium acetate trihydrate, 0.3 M Tris-HCl (pH 7.0) |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Sep 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.91→20 Å / Num. obs: 54418 / % possible obs: 96.2 % / Redundancy: 3.6 % / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.91→3.01 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.1 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4tvu Resolution: 2.93→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.879 / SU B: 22.359 / SU ML: 0.398 / Cross valid method: THROUGHOUT / ESU R Free: 0.474 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.392 Å2
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Refinement step | Cycle: 1 / Resolution: 2.93→20 Å
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Refine LS restraints |
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