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Open data
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Basic information
Entry | Database: PDB / ID: 8iij | |||||||||
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Title | H109G mutant of uracil DNA glycosylase X | |||||||||
![]() | Type-4 uracil-DNA glycosylase | |||||||||
![]() | DNA BINDING PROTEIN / UdgX / H109G / Mutant / Protein | |||||||||
Function / homology | ![]() uracil DNA N-glycosylase activity / 4 iron, 4 sulfur cluster binding / DNA repair / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Aroli, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mutational and structural analyses of UdgX: insights into the active site pocket architecture and its evolution. Authors: Aroli, S. / Woo, E.J. / Gopal, B. / 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 | ![]() | 55 KB | Display | ![]() |
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PDB format | ![]() | 36.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 13.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8iieC ![]() 8iifC ![]() 8iigC ![]() 8iihC ![]() 8iiiC ![]() 8iilC ![]() 8iimC ![]() 8iinC ![]() 8iioC ![]() 8iipC ![]() 8iiqC ![]() 8iirC ![]() 8iisC ![]() 8iitC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 21891.875 Da / Num. of mol.: 1 / Mutation: H109G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: MC2 155 / Gene: MSMEG_0265 / Plasmid: pET14b / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-SF4 / |
#3: Chemical | ChemComp-BME / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.43 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 7 Details: 2.0M Ammonium citrate tribasic pH7.0, 0.1M BIS-TRIS propane pH7.0 PH range: 6.8-7.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 17, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→29.1 Å / Num. obs: 16704 / % possible obs: 96.9 % / Redundancy: 5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.071 / Rrim(I) all: 0.117 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.83→1.87 Å / Redundancy: 5 % / Rmerge(I) obs: 0.815 / Num. unique obs: 978 / CC1/2: 0.52 / Rpim(I) all: 0.634 / Rrim(I) all: 1.036 / % possible all: 93.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 1.83→24.35 Å
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Refine LS restraints |
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LS refinement shell |
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