+Open data
-Basic information
Entry | Database: PDB / ID: 8ain | ||||||
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Title | MCUGI SAUNG complex | ||||||
Components |
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Keywords | PROTEIN BINDING / Ugi / Ung / complex / inhibitor | ||||||
Function / homology | Function and homology information uracil-DNA glycosylase / uracil DNA N-glycosylase activity / base-excision repair / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) Macrococcus caseolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Muselmani, W. / Savva, R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Viruses / Year: 2023 Title: A Multimodal Approach towards Genomic Identification of Protein Inhibitors of Uracil-DNA Glycosylase. Authors: Muselmani, W. / Kashif-Khan, N. / Bagneris, C. / Santangelo, R. / Williams, M.A. / Savva, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ain.cif.gz | 141 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ain.ent.gz | 107.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ain.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/8ain ftp://data.pdbj.org/pub/pdb/validation_reports/ai/8ain | HTTPS FTP |
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-Related structure data
Related structure data | 8ailC 8aimC 3wdgS S: Starting model for refinement 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: 26071.443 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: ung, A6762_02745, C7P97_05245, CSC87_03540, CV021_15850, E3A28_05745, E3K14_03025, GO782_00930, GO788_12235, NCTC6133_00684, NCTC7878_01215, NCTC7972_01353, QU38_09915, SAMEA70245418_01578 Production host: Escherichia coli (E. coli) / References: UniProt: A0A5F0HLK2, uracil-DNA glycosylase |
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#2: Protein | Mass: 14146.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macrococcus caseolyticus (bacteria) / Production host: Escherichia coli (E. coli) |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.41 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop Details: 1 M ammonium sulphate, 0.2 M sodium chloride, 9.55%(w/v) PEG 20.000, 0.1 M MES, at pH 6.5 |
-Data collection
Diffraction | Mean temperature: 289.15 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9198 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9198 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→45.8 Å / Num. obs: 11391 / % possible obs: 100 % / Redundancy: 11.9 % / CC1/2: 0.993 / Net I/σ(I): 2.12 |
Reflection shell | Resolution: 2.7→2.83 Å / Num. unique obs: 1470 / CC1/2: 0.55 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WDG Resolution: 2.7→45.8 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / SU B: 16.126 / SU ML: 0.315 / Cross valid method: FREE R-VALUE / ESU R: 1.2 / ESU R Free: 0.357 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.431 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→45.8 Å
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Refine LS restraints |
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LS refinement shell |
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