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- PDB-4ho2: Crystal structure of glucose 1-phosphate thymidylyltransferase fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ho2 | ||||||
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Title | Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with thymidine | ||||||
![]() | Glucose-1-phosphate thymidylyltransferase | ||||||
![]() | TRANSFERASE / thymidylyltransferase / nucleotide binding | ||||||
Function / homology | ![]() glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / extracellular polysaccharide biosynthetic process / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, T.J. / Chien, W.T. / Lin, C.C. / Wang, W.C. | ||||||
![]() | ![]() Title: Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with thymidine Authors: Chen, T.J. / Chien, W.T. / Lin, C.C. / Wang, W.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.5 KB | Display | ![]() |
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PDB format | ![]() | 56 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.7 KB | Display | ![]() |
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Full document | ![]() | 460.7 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 21.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1h5rS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Gene: rmlA / Plasmid: pTXB1 / Production host: ![]() ![]() References: UniProt: Q9AGY4, glucose-1-phosphate thymidylyltransferase | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M sodium cacodylate, 2.0M lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 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: 1.84→30 Å / Num. all: 26525 / Num. obs: 26483 / % possible obs: 99.5 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.042 |
Reflection shell | Resolution: 1.84→1.91 Å / Redundancy: 13 % / Rmerge(I) obs: 0.357 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1H5R Resolution: 1.84→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.919 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.137 / 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: 70.33 Å2 / Biso mean: 30.1519 Å2 / Biso min: 16.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.888 Å / Total num. of bins used: 20
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