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Open data
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Basic information
Entry | Database: PDB / ID: 7cd6 | ||||||
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Title | mAPE1-recessed dsDNA product complex | ||||||
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![]() | HYDROLASE/DNA / APE1 / protein-nucleic acid interaction / exonuclease / DNA repair / DNA BINDING PROTEIN / HYDROLASE-DNA complex | ||||||
Function / homology | ![]() Resolution of Abasic Sites (AP sites) / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / PCNA-Dependent Long Patch Base Excision Repair / : / POLB-Dependent Long Patch Base Excision Repair / Displacement of DNA glycosylase by APEX1 / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair ...Resolution of Abasic Sites (AP sites) / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / PCNA-Dependent Long Patch Base Excision Repair / : / POLB-Dependent Long Patch Base Excision Repair / Displacement of DNA glycosylase by APEX1 / 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 / negative regulation of smooth muscle cell migration / DNA-(abasic site) binding / : / double-stranded DNA exodeoxyribonuclease activity / : / double-stranded telomeric DNA binding / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / phosphoric diester hydrolase activity / cellular response to peptide hormone stimulus / 3'-5'-DNA exonuclease activity / NF-kappaB binding / positive regulation of G1/S transition of mitotic cell cycle / cellular response to cAMP / DNA-(apurinic or apyrimidinic site) endonuclease activity / regulation of mRNA stability / RNA endonuclease activity / 3'-5' exonuclease activity / telomere maintenance / cell redox homeostasis / base-excision repair / chromatin DNA binding / cellular response to hydrogen peroxide / regulation of apoptotic process / DNA recombination / transcription regulator complex / damaged DNA binding / transcription coactivator activity / oxidoreductase activity / nuclear speck / response to xenobiotic stimulus / DNA repair / centrosome / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, T.C. / Hsiao, Y.Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: APE1 distinguishes DNA substrates in exonucleolytic cleavage by induced space-filling. Authors: Liu, T.C. / Lin, C.T. / Chang, K.C. / Guo, K.W. / Wang, S. / Chu, J.W. / Hsiao, Y.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.4 KB | Display | ![]() |
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PDB format | ![]() | 105.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.1 KB | Display | ![]() |
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Full document | ![]() | 438.3 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7cd5C ![]() 1hd7S 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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Unit cell |
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Components
#1: Protein | Mass: 34683.359 Da / Num. of mol.: 1 / Mutation: deletion of 30 amino acids on the N-terminus Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P28352, Hydrolases; Acting on ester bonds |
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#2: DNA chain | Mass: 2739.824 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.15 Å3/Da / Density % sol: 70.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M Lithium sulfate monohydrate, 0.1M Na citrate tribasic dihydrate pH 5.5, 20% w/v Polyethylene glycol 1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 6, 2018 / Details: LN2-Cooled Fixed-Exit Double | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99984 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→30 Å / Num. obs: 17975 / % possible obs: 99.9 % / Redundancy: 17 % / Biso Wilson estimate: 51.47 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.026 / Rrim(I) all: 0.116 / Χ2: 1.161 / Net I/σ(I): 7.4 / Num. measured all: 305693 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1HD7 Resolution: 2.701→29.94 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 22.84 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 175.47 Å2 / Biso mean: 57.5741 Å2 / Biso min: 30.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.701→29.94 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -29.8695 Å / Origin y: -35.8203 Å / Origin z: 21.0115 Å
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Refinement TLS group |
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