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- PDB-1otp: STRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1otp | ||||||
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Title | STRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUCES AN ACTIVE CONFORMATION OF THYMIDINE PHOSPHORYLASE | ||||||
![]() | THYMIDINE PHOSPHORYLASE | ||||||
![]() | PHOSPHORYLASE / PYRIMIDINE METABOLISM / SALVAGE PATHWAY / DOMAIN MOVEMENT / TRANSFERASE / GLYCOSYLTRANSFERASE | ||||||
Function / homology | ![]() thymidine phosphorylase / pyrimidine nucleoside metabolic process / pyrimidine-nucleoside phosphorylase activity / thymidine metabolic process / thymidine phosphorylase activity / pyrimidine nucleobase metabolic process / 1,4-alpha-oligoglucan phosphorylase activity / AMP catabolic process / DNA damage response / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Pugmire, M.J. / Cook, W.J. / Jasanoff, A. / Walter, M.R. / Ealick, S.E. | ||||||
![]() | ![]() Title: Structural and theoretical studies suggest domain movement produces an active conformation of thymidine phosphorylase. Authors: Pugmire, M.J. / Cook, W.J. / Jasanoff, A. / Walter, M.R. / Ealick, S.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.3 KB | Display | ![]() |
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PDB format | ![]() | 70 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 414.1 KB | Display | ![]() |
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Full document | ![]() | 421.6 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 22 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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 natural source / Source: (natural) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.4 Details: PROTEIN WAS CRYSTALLIZED FROM 0.9 - 1.2 M SODIUM CITRATE (PH 6.4 - 6.8) AND 2MM DTT AT ROOM TEMPERATURE USING HANGING DROP METHOD PH range: 6.4-6.8 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 1, 1990 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→79.5 Å / Num. obs: 14713 / % possible obs: 87.3 % / Rsym value: 0.071 |
Reflection shell | Resolution: 2.58→2.67 Å / % possible all: 65.2 |
Reflection | *PLUS Num. measured all: 57343 / Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS % possible obs: 65.2 % |
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Processing
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Refinement | Method to determine structure: SINGLE ISOMORPHOUS REPLACEMENT Resolution: 2.8→8 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 30.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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