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Yorodumi- PDB-1azy: STRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1azy | ||||||
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Title | STRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUCES AN ACTIVE CONFORMATION OF THYMIDINE PHOSPHORYLASE | ||||||
Components | THYMIDINE PHOSPHORYLASE | ||||||
Keywords | GLYCOSYLTRANSFERASE / THYMIDINE PHOSPHORYLASE / SALVAGE PATHWAY | ||||||
Function / homology | Function and homology information 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 / DNA damage response / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 3 Å | ||||||
Authors | Pugmire, M.J. / Cook, W.J. / Jasanoff, A. / Walter, M.R. / Ealick, S.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 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. #1: 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 | 1azy.cif.gz | 154.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1azy.ent.gz | 125.2 KB | Display | PDB format |
PDBx/mmJSON format | 1azy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1azy_validation.pdf.gz | 421.2 KB | Display | wwPDB validaton report |
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Full document | 1azy_full_validation.pdf.gz | 436.7 KB | Display | |
Data in XML | 1azy_validation.xml.gz | 31.3 KB | Display | |
Data in CIF | 1azy_validation.cif.gz | 41.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/1azy ftp://data.pdbj.org/pub/pdb/validation_reports/az/1azy | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.997688, -0.063888, 0.023166), Vector: |
-Components
#1: Protein | Mass: 47240.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: MONOCLINIC CRYSTAL FORM / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P07650, thymidine phosphorylase |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.7 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: pH 4.6 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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 | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: NICOLET / Detector: AREA DETECTOR / Date: Jan 1, 1990 |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30.7 Å / Num. obs: 22922 / % possible obs: 95.7 % / Rsym value: 0.102 |
Reflection shell | Resolution: 2.79→2.89 Å / % possible all: 72.8 |
Reflection | *PLUS Num. measured all: 81699 / Rmerge(I) obs: 0.101 |
Reflection shell | *PLUS % possible obs: 72.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 3→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 31.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS / Rms dev position: 3 Å / Weight position: 250 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.13 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.213 / Rfactor Rfree: 0.271 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.28 |