+Open data
-Basic information
Entry | Database: PDB / ID: 6l5b | ||||||
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Title | The structure of the UdgX mutant H109E at a post-excision state | ||||||
Components | Uracil DNA glycosylase superfamily protein | ||||||
Keywords | DNA BINDING PROTEIN / UdgX / covalent complex / protein-DNA interaction / DNA repair / glycosylase | ||||||
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: 2.00004990268 Å | ||||||
Authors | Xie, W. / Tu, J. / Zeng, H. | ||||||
Funding support | China, 1items
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Citation | Journal: DNA Repair (Amst) / Year: 2021 Title: Structural insights into an MsmUdgX mutant capable of both crosslinking and uracil excision capability. Authors: Jia, Q. / Zeng, H. / Tu, J. / Sun, L. / Cao, W. / Xie, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l5b.cif.gz | 66.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l5b.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 6l5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/6l5b ftp://data.pdbj.org/pub/pdb/validation_reports/l5/6l5b | HTTPS FTP |
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-Related structure data
Related structure data | 6l5aC 6l6sC 6io9S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 23249.420 Da / Num. of mol.: 1 / Fragment: UNP residues 1-208 / Mutation: H109E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Strain: MC2 155 / Gene: MSMEG_0265 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QP43 |
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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: 1.71 Å3/Da / Density % sol: 28.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.15M sodium malonate pH 7.0 and 3.8% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Apr 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→21.275 Å / Num. obs: 10298 / % possible obs: 96.8 % / Redundancy: 2.5 % / Biso Wilson estimate: 16.7493772562 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1484 / CC1/2: 0.919 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IO9 Resolution: 2.00004990268→21.2749731543 Å / SU ML: 0.1456086395 / Cross valid method: FREE R-VALUE / σ(F): 1.3553838805 / Phase error: 21.1937260771
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.7855530388 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.00004990268→21.2749731543 Å
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Refine LS restraints |
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LS refinement shell |
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