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- PDB-7a1f: Crystal structure of human 5' exonuclease Appollo in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7a1f | ||||||
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Title | Crystal structure of human 5' exonuclease Appollo in complex with 5'dAMP | ||||||
![]() | 5' exonuclease Apollo | ||||||
![]() | LYASE / DCLRE1B / SNM1B / exonuclease / Apollo | ||||||
Function / homology | ![]() telomeric 3' overhang formation / telomeric loop formation / protection from non-homologous end joining at telomere / telomere maintenance via telomere lengthening / 5'-3' exonuclease activity / telomere capping / 5'-3' DNA exonuclease activity / interstrand cross-link repair / telomere maintenance / Fanconi Anemia Pathway ...telomeric 3' overhang formation / telomeric loop formation / protection from non-homologous end joining at telomere / telomere maintenance via telomere lengthening / 5'-3' exonuclease activity / telomere capping / 5'-3' DNA exonuclease activity / interstrand cross-link repair / telomere maintenance / Fanconi Anemia Pathway / double-strand break repair via nonhomologous end joining / beta-lactamase activity / beta-lactamase / chromosome, telomeric region / damaged DNA binding / Hydrolases; Acting on ester bonds / nuclear body / centrosome / protein-containing complex binding / protein homodimerization activity / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Newman, J.A. / Baddock, H.T. / Mukhopadhyay, S.M.M. / Burgess-Brown, N.A. / von Delft, F. / Arrowshmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A phosphate binding pocket is a key determinant of exo- versus endo-nucleolytic activity in the SNM1 nuclease family. Authors: Baddock, H.T. / Newman, J.A. / Yosaatmadja, Y. / Bielinski, M. / Schofield, C.J. / Gileadi, O. / McHugh, P.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.6 KB | Display | ![]() |
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PDB format | ![]() | 125.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 32.3 KB | Display | |
Data in CIF | ![]() | 47.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7b2xC ![]() 7b9bC ![]() 5ahoS 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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Unit cell |
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Components
#1: Protein | Mass: 38657.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9H816, Hydrolases; Acting on ester bonds #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-D5M / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M Ammonium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2017 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.8→68.65 Å / Num. obs: 55714 / % possible obs: 93.3 % / Redundancy: 2.2 % / Biso Wilson estimate: 23.76 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.051 / Rrim(I) all: 0.081 / Net I/σ(I): 7.9 / Num. measured all: 123105 / Scaling rejects: 3 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 2.3 %
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5AHO Resolution: 1.8→43.953 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 27.85 / 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: 93.6 Å2 / Biso mean: 31.9746 Å2 / Biso min: 13.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→43.953 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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