+Open data
-Basic information
Entry | Database: PDB / ID: 7b2x | ||||||
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Title | Crystal structure of human 5' exonuclease Appollo H61Y variant | ||||||
Components | 5' exonuclease Apollo | ||||||
Keywords | LYASE / DCLRE1B / SNM1B / exonuclease / Apollo | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | 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 | United Kingdom, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b2x.cif.gz | 90.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b2x.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 7b2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b2x_validation.pdf.gz | 432.4 KB | Display | wwPDB validaton report |
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Full document | 7b2x_full_validation.pdf.gz | 434.4 KB | Display | |
Data in XML | 7b2x_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 7b2x_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/7b2x ftp://data.pdbj.org/pub/pdb/validation_reports/b2/7b2x | HTTPS FTP |
-Related structure data
Related structure data | 7a1fC 7b9bC 5ahoS 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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Unit cell |
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-Components
#1: Protein | Mass: 38138.855 Da / Num. of mol.: 1 / Mutation: H61Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DCLRE1B, SNM1B / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9H816, Hydrolases; Acting on ester bonds |
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#2: Chemical | ChemComp-NI / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 22% PEG3350 -- 0.1M HEPES pH 7.0 -- 0.2M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→45.4 Å / Num. obs: 8386 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 104.61 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.15 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 3.1→3.31 Å / Rmerge(I) obs: 2.17 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1474 / CC1/2: 0.58 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5aho Resolution: 3.1→45.37 Å / SU ML: 0.5497 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.6023 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 91.98 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→45.37 Å
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Refine LS restraints |
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LS refinement shell |
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