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- PDB-4qfy: Crystal structure of the tetrameric dGTP/dCTP-bound SAMHD1 (RN206... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qfy | ||||||
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Title | Crystal structure of the tetrameric dGTP/dCTP-bound SAMHD1 (RN206) mutant catalytic core | ||||||
![]() | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | ||||||
![]() | HYDROLASE / deoxynucleoside triphosphate triphosphohydrolase / 2'-deoxynucleotide-5'-triphosphate / HIV restriction factor / dNTPase | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Koharudin, L.M.I. / Wu, Y. / DeLucia, M. / Mehrens, J. / Gronenborn, A.M. / Ahn, J. | ||||||
![]() | ![]() Title: Structural Basis of Allosteric Activation of Sterile alpha Motif and Histidine-Aspartate Domain-containing Protein 1 (SAMHD1) by Nucleoside Triphosphates. Authors: Koharudin, L.M. / Wu, Y. / DeLucia, M. / Mehrens, J. / Gronenborn, A.M. / Ahn, 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 | ![]() | 425.9 KB | Display | ![]() |
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PDB format | ![]() | 347.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.4 MB | Display | ![]() |
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Full document | ![]() | 4.4 MB | Display | |
Data in XML | ![]() | 76 KB | Display | |
Data in CIF | ![]() | 100.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4qfxC ![]() 4qfzC ![]() 4qg0C ![]() 4qg1C ![]() 4qg2C ![]() 4qg4C ![]() 4bzbS 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: 63426.375 Da / Num. of mol.: 4 / Fragment: UNP residues 113-626 / Mutation: H206R/D207N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases #2: Chemical | ChemComp-DGT / #3: Chemical | ChemComp-DCP / #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M SPG, pH 6.5, 25% PEG1500, 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 2, 2013 |
Radiation | Monochromator: Rosenbaum-Rock double-crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→38.672 Å / Num. all: 132888 / Num. obs: 132803 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.68 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 7.68 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BZB Resolution: 2.1→38.672 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 31.26 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→38.672 Å
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Refine LS restraints |
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LS refinement shell |
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