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- PDB-5grk: Crystal structure of Uracil DNA glycosylase -Xanthine complex fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5grk | ||||||
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Title | Crystal structure of Uracil DNA glycosylase -Xanthine complex from Bradyrhizobium diazoefficiens | ||||||
![]() | Blr0248 protein | ||||||
![]() | HYDROLASE / Uracil DNA glycosylase (UDG) Bradyrhizobium diazoefficiens / nitrogen fixing symbiont / DNA repair / Xanthine. | ||||||
Function / homology | Uracil-DNA glycosylase-like domain superfamily / XANTHINE / Blr0248 protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Patil, V.V. / Ullas, V.C. / Ahn, W. / Varshney, U. / Woo, E. | ||||||
![]() | ![]() Title: Uracil DNA glycosylase (UDG) activities in Bradyrhizobium diazoefficiens: characterization of a new class of UDG with broad substrate specificity Authors: Chembazhi, U.V. / Patil, V.V. / Sah, S. / Reeve, W. / Tiwari, R.P. / Woo, E. / Varshney, U. #1: Journal: NUCLEIC ACIDS RES. / Year: 2015 Title: A unique uracil-DNA binding protein of the uracil DNA glycosylase superfamily Authors: Sang, P.B. / Srinath, T. / Patil, A.G. / Woo, E. / Varshney, U. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 382.9 KB | Display | ![]() |
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PDB format | ![]() | 330.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29725.795 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: USDA 110 / Gene: blr0248 / Production host: ![]() ![]() #2: Chemical | ChemComp-XAN / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 20% PEG3350, 200 mM sodium citrate, 100 mM sodium citrate/citric acid |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.804→47.174 Å / Num. obs: 40422 / % possible obs: 99.91 % / Redundancy: 13.2 % / Net I/σ(I): 15.13 |
Reflection shell | Resolution: 2.8→2.85 Å |
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Processing
Software | Name: PHENIX / Version: 1.9_1692 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.804→47.174 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.804→47.174 Å
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Refine LS restraints |
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LS refinement shell |
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