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Yorodumi- PDB-4ho6: Crystal structure of glucose 1-phosphate thymidylyltransferase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ho6 | ||||||
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Title | Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with UDP-glucose and UTP | ||||||
Components | Glucose-1-phosphate thymidylyltransferase | ||||||
Keywords | TRANSFERASE / thymidylyltransferase / nucleotide binding | ||||||
Function / homology | Function and homology information glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / extracellular polysaccharide biosynthetic process / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Aneurinibacillus thermoaerophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Chen, T.J. / Chien, W.T. / Lin, C.C. / Wang, W.C. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with UDP-glucose and UTP Authors: Chen, T.J. / Chien, W.T. / Lin, C.C. / Wang, W.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ho6.cif.gz | 78.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ho6.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ho6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/4ho6 ftp://data.pdbj.org/pub/pdb/validation_reports/ho/4ho6 | HTTPS FTP |
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-Related structure data
Related structure data | 1h5rS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 32973.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aneurinibacillus thermoaerophilus (bacteria) Gene: rmlA / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) References: UniProt: Q9AGY4, glucose-1-phosphate thymidylyltransferase | ||
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#2: Chemical | ChemComp-UPG / | ||
#3: Chemical | ChemComp-UTP / | ||
#4: Chemical | #5: 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: 2.15 Å3/Da / Density % sol: 42.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M sodium cacodylate, 2.7M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2011 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.92→30 Å / Num. obs: 22509 / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.056 / Χ2: 1.033 / Net I/σ(I): 13.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1H5R Resolution: 1.92→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.272 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.37 Å2 / Biso mean: 28.6918 Å2 / Biso min: 14.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.97 Å / Total num. of bins used: 20
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