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- PDB-1brw: THE CRYSTAL STRUCTURE OF PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE IN A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1brw | ||||||
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Title | THE CRYSTAL STRUCTURE OF PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE IN A CLOSED CONFORMATION | ||||||
![]() | PROTEIN (PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE) | ||||||
![]() | TRANSFERASE / NUCLEOSIDE PHOSPHORYLASE / DOMAIN MOVEMENT | ||||||
Function / homology | ![]() pyrimidine-nucleoside phosphorylase / pyrimidine nucleoside metabolic process / pyrimidine-nucleoside phosphorylase activity / thymidine phosphorylase activity / pyrimidine nucleobase metabolic process / 1,4-alpha-oligoglucan phosphorylase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pugmire, M.J. / Ealick, S.E. | ||||||
![]() | ![]() Title: The crystal structure of pyrimidine nucleoside phosphorylase in a closed conformation. Authors: Pugmire, M.J. / 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 | ![]() | 173.4 KB | Display | ![]() |
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PDB format | ![]() | 136.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2tptS 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46063.184 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P77836, pyrimidine-nucleoside phosphorylase |
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-Non-polymers , 5 types, 117 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/URA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/URA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-URA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: 0.1 M MES PH 6.0-6.2 25% PEG 6000 PSEUDOURIDINE AT 10X PROTEIN CONCENTRATION | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop / Details: Zhou, M., (1998) Acta Cryst., D55, 287. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC / Detector: CCD / Date: Feb 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 55716 / % possible obs: 88.4 % / Redundancy: 2.9 % / Rsym value: 0.067 |
Reflection | *PLUS Num. measured all: 396276 / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 41.7 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.232 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2TPT Resolution: 2.1→30 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 26.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.2 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 30 Å / σ(F): 2 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 26.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % reflection Rfree: 8.6 % |