+Open data
-Basic information
Entry | Database: PDB / ID: 8d9j | |||||||||||||||
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Title | SAMHD1-DNA complex | |||||||||||||||
Components |
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Keywords | HYDROLASE/DNA / DNA complex / catalytic domain / dNTP hydrolysis / ANTIVIRAL PROTEIN / HYDROLASE-DNA complex | |||||||||||||||
Function / homology | Function and homology information Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / triphosphoric monoester hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / DNA strand resection involved in replication fork processing / deoxyribonucleotide catabolic process ...Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / triphosphoric monoester hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / DNA strand resection involved in replication fork processing / deoxyribonucleotide catabolic process / dGTP catabolic process / negative regulation of type I interferon-mediated signaling pathway / regulation of innate immune response / somatic hypermutation of immunoglobulin genes / RNA nuclease activity / double-strand break repair via homologous recombination / Interferon alpha/beta signaling / site of double-strand break / single-stranded DNA binding / protein homotetramerization / defense response to virus / nucleic acid binding / immune response / innate immune response / DNA damage response / GTP binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å | |||||||||||||||
Authors | Hollis, T.J. / Batalis, S.M. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: To Be Published Title: SAMHD1-DNA complex Authors: Hollis, T.J. / Batalis, S.M. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d9j.cif.gz | 467.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d9j.ent.gz | 301.7 KB | Display | PDB format |
PDBx/mmJSON format | 8d9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8d9j_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 8d9j_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 8d9j_validation.xml.gz | 62.5 KB | Display | |
Data in CIF | 8d9j_validation.cif.gz | 85.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/8d9j ftp://data.pdbj.org/pub/pdb/validation_reports/d9/8d9j | HTTPS FTP |
-Related structure data
Related structure data | 8d94C 3u1nS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 72305.414 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SAMHD1, MOP5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star(DE3) References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases #2: DNA chain | Mass: 1504.037 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-FE / #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM Tris-HCl pH 7.5, 150 mM CaCl2, 20% PEG 3350, and 4% 2-methyl-2,4-pentanediol (MPD) Temp details: Room Temperature |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.82→50 Å / Num. obs: 47336 / % possible obs: 99.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 55.39 Å2 / CC1/2: 0.98 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.85→2.93 Å / Redundancy: 6.5 % / Num. unique obs: 3958 / CC1/2: 0.55 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3u1n Resolution: 2.82→39.05 Å / SU ML: 0.3321 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2736 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.82→39.05 Å
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Refine LS restraints |
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LS refinement shell |
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