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Yorodumi- PDB-6ail: CRYSTAL STRUCTURE AT 1.3 ANGSTROMS RESOLUTION OF A NOVEL UDG, Udg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ail | ||||||
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Title | CRYSTAL STRUCTURE AT 1.3 ANGSTROMS RESOLUTION OF A NOVEL UDG, UdgX, FROM Mycobacterium smegmatis | ||||||
Components | Uracil DNA glycosylase X | ||||||
Keywords | DNA BINDING PROTEIN / DNA repair / Base excision / DNA-Protein crosslink. | ||||||
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 | Mycobacterium smegmatis str. MC2 155 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.335 Å | ||||||
Authors | Ahn, W.C. / Aroli, S. / Varshney, V. / Woo, E.J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2019 Title: Covalent binding of uracil DNA glycosylase UdgX to abasic DNA upon uracil excision. Authors: Ahn, W.C. / Aroli, S. / Kim, J.H. / Moon, J.H. / Lee, G.S. / Lee, M.H. / Sang, P.B. / Oh, B.H. / Varshney, U. / Woo, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ail.cif.gz | 125.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ail.ent.gz | 96.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ail.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ail_validation.pdf.gz | 438.2 KB | Display | wwPDB validaton report |
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Full document | 6ail_full_validation.pdf.gz | 439.6 KB | Display | |
Data in XML | 6ail_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 6ail_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/6ail ftp://data.pdbj.org/pub/pdb/validation_reports/ai/6ail | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24372.654 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Asp165, Asp166, and Pro209 could not be modeled. Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria) Strain: MC2 155 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0QP43 |
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#2: Chemical | ChemComp-SF4 / |
#3: Water | ChemComp-HOH / |
-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: 39.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 2.0M Ammonium citrate tribasic pH7.0, 0.1M BIS-TRIS propane pH7.0 |
-Data collection
Diffraction | Mean temperature: 190 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.335→50 Å / Num. obs: 42217 / % possible obs: 96.2 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 55.74 |
Reflection shell | Resolution: 1.34→1.36 Å / Rmerge(I) obs: 0.187 / Num. unique obs: 1864 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.335→28.106 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 13.37 / 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: 1.335→28.106 Å
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Refine LS restraints |
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LS refinement shell |
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