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- PDB-5gn3: Structure of selenomethionine-labelled Uracil DNA glycosylase (Bd... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gn3 | ||||||
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Title | Structure of selenomethionine-labelled Uracil DNA glycosylase (BdiUNG) from Bradyrhizobium diazoefficiens | ||||||
![]() | Blr0248 protein | ||||||
![]() | HYDROLASE / Uracil DNA glycosylase (UDG) / Bradyrhizobium diazoefficiens / nitrogen fixing symbiont | ||||||
Function / homology | Uracil-DNA glycosylase-like domain superfamily / Blr0248 protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Patil, V.V. / Chembazhi, U.V. / 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 | ![]() | 224.4 KB | Display | ![]() |
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PDB format | ![]() | 189 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.2 KB | Display | ![]() |
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Full document | ![]() | 466.7 KB | Display | |
Data in XML | ![]() | 45.6 KB | Display | |
Data in CIF | ![]() | 65.6 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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Unit cell |
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Components
#1: Protein | Mass: 29960.271 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: USDA 110 / Gene: blr0248 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64.06 % Description: the entry contains Friedel pairs in F_Plus/Minus columns |
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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: Jul 10, 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: 2.281→30.99 Å / Num. obs: 132492 / % possible obs: 91.73 % / Redundancy: 7 % / Net I/σ(I): 21.39 |
Reflection shell | Resolution: 2.281→2.32 Å |
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Processing
Software | Name: PHENIX / Version: 1.9_1692 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Details: the entry contains Friedel pairs in F_Plus/Minus columns
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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: 2.281→30.99 Å
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Refine LS restraints |
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LS refinement shell |
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