+Open data
-Basic information
Entry | Database: PDB / ID: 8iis | |||||||||
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Title | MsmUdgX H109S/R184A double mutant | |||||||||
Components | Type-4 uracil-DNA glycosylase | |||||||||
Keywords | DNA BINDING PROTEIN / UdgX / H109S / R184A / mutant / protein | |||||||||
Function / homology | Function and homology information uracil DNA N-glycosylase activity / 4 iron, 4 sulfur cluster binding / DNA repair / metal ion binding Similarity search - Function | |||||||||
Biological species | Mycolicibacterium smegmatis MC2 155 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | |||||||||
Authors | Aroli, S. | |||||||||
Funding support | India, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8iis.cif.gz | 59 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8iis.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 8iis.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8iis_validation.pdf.gz | 927.5 KB | Display | wwPDB validaton report |
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Full document | 8iis_full_validation.pdf.gz | 928.8 KB | Display | |
Data in XML | 8iis_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 8iis_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/8iis ftp://data.pdbj.org/pub/pdb/validation_reports/ii/8iis | HTTPS FTP |
-Related structure data
Related structure data | 8iieC 8iifC 8iigC 8iihC 8iiiC 8iijC 8iilC 8iimC 8iinC 8iioC 8iipC 8iiqC 8iirC 8iitC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22615.719 Da / Num. of mol.: 1 / Mutation: H109S, R184A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Strain: MC2 155 / Gene: MSMEG_0265 / Plasmid: pET14b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0QP43, uracil-DNA glycosylase |
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#2: Chemical | ChemComp-SF4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 43.81 % |
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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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 23, 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: 1.6→28.11 Å / Num. obs: 24280 / % possible obs: 94.3 % / Redundancy: 4.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.031 / Rrim(I) all: 0.051 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.059 / Mean I/σ(I) obs: 16.8 / Num. unique obs: 831 / CC1/2: 0.985 / Rpim(I) all: 0.046 / Rrim(I) all: 0.076 / % possible all: 66.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→23.48 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 15.07 / Stereochemistry target values: MLHL
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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: 1.61→23.48 Å
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Refine LS restraints |
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LS refinement shell |
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