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Yorodumi- PDB-2ggo: Crystal Structure of glucose-1-phosphate thymidylyltransferase fr... -
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-Basic information
Entry | Database: PDB / ID: 2ggo | ||||||
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Title | Crystal Structure of glucose-1-phosphate thymidylyltransferase from Sulfolobus tokodaii | ||||||
Components | 401aa long hypothetical glucose-1-phosphate thymidylyltransferase | ||||||
Keywords | TRANSFERASE / BETA BARREL | ||||||
Function / homology | Function and homology information galactosamine-1-phosphate N-acetyltransferase / UDP-N-acetylgalactosamine diphosphorylase / UDP-N-acetylgalactosamine diphosphorylase activity / UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / UDP-N-acetylglucosamine diphosphorylase ...galactosamine-1-phosphate N-acetyltransferase / UDP-N-acetylgalactosamine diphosphorylase / UDP-N-acetylgalactosamine diphosphorylase activity / UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Sulfolobus tokodaii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 1.8 Å | ||||||
Authors | Rajakannan, V. / Mizushima, T. / Suzuki, A. / Masui, R. / Kuramitsu, S. / Yamane, T. | ||||||
Citation | Journal: To be published Title: Crystal Structure of glucose-1-phosphate thymidylyltransferase from Sulfolobus tokodaii Authors: Rajakannan, V. / Yamane, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ggo.cif.gz | 90.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ggo.ent.gz | 73.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ggo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/2ggo ftp://data.pdbj.org/pub/pdb/validation_reports/gg/2ggo | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 44573.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Production host: Escherichia coli (E. coli) References: GenBank: 15621447, UniProt: Q975F9*PLUS, glucose-1-phosphate thymidylyltransferase |
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#2: 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: 3.1 Å3/Da / Density % sol: 60.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 10% PEG 3350, 0.5M CsCl, 20mM TRIS-HCL, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 3, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 49579 / Num. obs: 48014 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.074 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 90.2 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.8→19 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.134 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.952 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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