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Open data
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Basic information
Entry | Database: PDB / ID: 5wn5 | ||||||
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Title | APE1 exonuclease substrate complex with a C/T mismatch and Mn2+ | ||||||
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Function / homology | ![]() Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / positive regulation of gene expression via chromosomal CpG island demethylation / double-stranded telomeric DNA binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Freudenthal, B.D. / Whitaker, A.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular snapshots of APE1 proofreading mismatches and removing DNA damage. Authors: Whitaker, A.M. / Flynn, T.S. / Freudenthal, B.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 152 KB | Display | ![]() |
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PDB format | ![]() | 114.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5wn0C ![]() 5wn1C ![]() 5wn2C ![]() 5wn3C ![]() 5wn4C ![]() 5dffS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-DNA chain , 3 types, 3 molecules CDE
#1: DNA chain | Mass: 3334.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 3077.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 6424.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein , 1 types, 2 molecules AB
#4: Protein | ![]() Mass: 31156.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P27695, ![]() ![]() |
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-Non-polymers , 4 types, 165 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/NA.gif)
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![](data/chem/img/HOH.gif)
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#5: Chemical | #6: Chemical | ChemComp-NA / | #7: Chemical | ![]() #8: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.57 % / Mosaicity: 0.999 ° |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→25 Å / Num. obs: 74865 / % possible obs: 99.8 % / Redundancy: 11.2 % / Biso Wilson estimate: 29.71 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.698 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 5DFF Resolution: 2.2→24.74 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.55
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→24.74 Å
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Refine LS restraints |
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LS refinement shell |
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