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Yorodumi- PDB-1tpt: THREE-DIMENSIONAL STRUCTURE OF THYMIDINE PHOSPHORYLASE FROM ESCHE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tpt | ||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF THYMIDINE PHOSPHORYLASE FROM ESCHERICHIA COLI AT 2.8 ANGSTROMS RESOLUTION | ||||||
Components | THYMIDINE PHOSPHORYLASE | ||||||
Keywords | THYMIDINE PHOSPHORYLASE | ||||||
Function / homology | Function and homology information thymidine phosphorylase / pyrimidine-nucleoside phosphorylase activity / pyrimidine nucleoside metabolic process / thymidine metabolic process / thymidine phosphorylase activity / pyrimidine nucleobase metabolic process / 1,4-alpha-oligoglucan phosphorylase activity / DNA damage response / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Walter, M.R. / Cook, W.J. / Cole, L.B. / Short, S.A. / Koszalka, G.W. / Krenitsky, T.A. / Ealick, S.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1990 Title: Three-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8 A resolution. Authors: Walter, M.R. / Cook, W.J. / Cole, L.B. / Short, S.A. / Koszalka, G.W. / Krenitsky, T.A. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tpt.cif.gz | 26 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tpt.ent.gz | 12.6 KB | Display | PDB format |
PDBx/mmJSON format | 1tpt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tpt_validation.pdf.gz | 313.5 KB | Display | wwPDB validaton report |
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Full document | 1tpt_full_validation.pdf.gz | 313.5 KB | Display | |
Data in XML | 1tpt_validation.xml.gz | 1 KB | Display | |
Data in CIF | 1tpt_validation.cif.gz | 4.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/1tpt ftp://data.pdbj.org/pub/pdb/validation_reports/tp/1tpt | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47240.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: P07650, thymidine phosphorylase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-TDR / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.06 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.5 / Method: vapor diffusion, hanging dropDetails: took from Cook, W.J.,(1987) J. Biol. Chem., 262, 3788. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.8 Å / Num. obs: 15034 / Num. measured all: 77819 / Rmerge F obs: 0.082 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||
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Refinement | Rfactor obs: 0.28 / Highest resolution: 2.8 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||
Refinement | *PLUS Rfactor obs: 0.28 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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