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- PDB-5itt: Crystal Structure of Human NEIL1 bound to duplex DNA containing THF -
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Open data
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Basic information
Entry | Database: PDB / ID: 5itt | ||||||||||||
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Title | Crystal Structure of Human NEIL1 bound to duplex DNA containing THF | ||||||||||||
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![]() | DNA BINDING PROTEIN/DNA / NEIL1 DNA Glycosylase base excision repair Fpg Nei / DNA BINDING PROTEIN-DNA complex | ||||||||||||
Function / homology | ![]() negative regulation of nuclease activity / Defective Base Excision Repair Associated with NEIL1 / depyrimidination / DNA N-glycosylase activity / hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA-(apurinic or apyrimidinic site) endonuclease activity ...negative regulation of nuclease activity / Defective Base Excision Repair Associated with NEIL1 / depyrimidination / DNA N-glycosylase activity / hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair, gap-filling / base-excision repair / chromosome / response to oxidative stress / damaged DNA binding / centrosome / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() unidentified (others) | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Zhu, C. / Lu, L. / Zhang, J. / Yue, Z. / Song, J. / Zong, S. / Liu, M. / Stovicek, O. / Gao, Y. / Yi, C. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair Authors: Zhu, C. / Lu, L. / Zhang, J. / Yue, Z. / Song, J. / Zong, S. / Liu, M. / Stovicek, O. / Gao, Y.Q. / Yi, C. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 214.6 KB | Display | ![]() |
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PDB format | ![]() | 163.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5itqC ![]() 5itrC ![]() 5ituC ![]() 5itxC ![]() 5ityC ![]() 1tdhS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44925.371 Da / Num. of mol.: 3 / Mutation: K242R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q96FI4, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase #2: DNA chain | Mass: 7949.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others) #3: DNA chain | | Mass: 7917.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others) #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.55 % |
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Crystal grow | Temperature: 288 K / Method: evaporation / pH: 6.5 Details: 0.1 M cacodylic acid (pH 7.0), 0.1 M NaCl, 0.05 M MgCl2 and 24% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Oct 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→91.81 Å / Num. obs: 43613 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.081 / Rsym value: 0.061 / Net I/σ(I): 19.23 |
Reflection shell | Resolution: 2.53→2.63 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1TDH Resolution: 2.53→81.81 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Refinement step | Cycle: LAST / Resolution: 2.53→81.81 Å
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LS refinement shell | Resolution: 2.529→2.595 Å / Total num. of bins used: 20
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