+Open data
-Basic information
Entry | Database: PDB / ID: 6cvs | ||||||
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Title | Human Aprataxin (Aptx) L248M bound to DNA, AMP and Zn product | ||||||
Components |
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Keywords | hydrolase/dna / protein-DNA complex / DNA repair / 5'-DNA end processing / Histidine Triad domain / HIT domain / Zinc-finger / 5'-DNA end recognition / HYDROLASE / hydrolase-dna-rna complex / hydrolase-dna complex | ||||||
Function / homology | Function and homology information adenosine-5'-diphospho-5'-[DNA] diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA 5'-adenosine monophosphate hydrolase activity / polynucleotide 3'-phosphatase activity / phosphoglycolate phosphatase activity / single-strand break-containing DNA binding / single strand break repair / mismatched DNA binding / DNA ligation ...adenosine-5'-diphospho-5'-[DNA] diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA 5'-adenosine monophosphate hydrolase activity / polynucleotide 3'-phosphatase activity / phosphoglycolate phosphatase activity / single-strand break-containing DNA binding / single strand break repair / mismatched DNA binding / DNA ligation / phosphoprotein binding / regulation of protein stability / double-stranded RNA binding / single-stranded DNA binding / double-stranded DNA binding / damaged DNA binding / chromatin binding / chromatin / nucleolus / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | Schellenberg, M.J. / Tumbale, P.S. / Williams, R.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: EMBO J. / Year: 2018 Title: Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease. Authors: Tumbale, P. / Schellenberg, M.J. / Mueller, G.A. / Fairweather, E. / Watson, M. / Little, J.N. / Krahn, J. / Waddell, I. / London, R.E. / Williams, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cvs.cif.gz | 299.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cvs.ent.gz | 244 KB | Display | PDB format |
PDBx/mmJSON format | 6cvs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/6cvs ftp://data.pdbj.org/pub/pdb/validation_reports/cv/6cvs | HTTPS FTP |
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-Related structure data
Related structure data | 6cvoC 6cvpC 6cvqC 6cvrC 6cvtC 4ndfS 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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2 |
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Unit cell |
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-Components
-Protein / DNA chain , 2 types, 6 molecules ABDEGH
#1: Protein | Mass: 21277.793 Da / Num. of mol.: 2 / Fragment: Aprataxin catalytic Domain / Mutation: L248M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APTX, AXA1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7Z2E3, EC: 3.1.11.7, EC: 3.1.12.2 #2: DNA chain | Mass: 3044.017 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Non-polymers , 4 types, 504 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.64 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 100 mM MES, 25% w/v polyethylene glycol 4000 / PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 3, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.11→50 Å / Num. obs: 31283 / % possible obs: 95.4 % / Redundancy: 4.7 % / Biso Wilson estimate: 30.37 Å2 / Rmerge(I) obs: 0.106 / Χ2: 0.995 / Net I/σ(I): 6.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NDF Resolution: 2.11→28.889 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.05
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.41 Å2 / Biso mean: 39.2242 Å2 / Biso min: 16.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.11→28.889 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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