+Open data
-Basic information
Entry | Database: PDB / ID: 4rxo | ||||||
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Title | The structure of GTP-bound SAMHD1 | ||||||
Components | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | ||||||
Keywords | HYDROLASE / HD-domain / dNTP and GTP binding / phosphorylation | ||||||
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 / deoxyribonucleotide catabolic process / dGTP 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 / deoxyribonucleotide catabolic process / dGTP catabolic process / DNA strand resection involved in replication fork processing / 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Zhu, C.F. / Wei, W. / Peng, X. / Dong, Y.H. / Gong, Y. / Yu, X.F. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: The mechanism of substrate-controlled allosteric regulation of SAMHD1 activated by GTP. Authors: Zhu, C.F. / Wei, W. / Peng, X. / Dong, Y.H. / Gong, Y. / Yu, X.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rxo.cif.gz | 380.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rxo.ent.gz | 306.6 KB | Display | PDB format |
PDBx/mmJSON format | 4rxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rxo_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 4rxo_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4rxo_validation.xml.gz | 63.6 KB | Display | |
Data in CIF | 4rxo_validation.cif.gz | 87.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/4rxo ftp://data.pdbj.org/pub/pdb/validation_reports/rx/4rxo | HTTPS FTP |
-Related structure data
Related structure data | 4rxpC 4rxqC 4rxrC 4rxsC 3u1nS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 114 - 583 / Label seq-ID: 27 - 496
NCS ensembles :
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-Components
#1: Protein | Mass: 62486.184 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) References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-GTP / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.59 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M sodium chloride, 0.1M Na/K phosphate, and 25% w/v polyethylene glycol 1000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 14, 2013 |
Radiation | Monochromator: cryocooled channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 67543 / Num. obs: 65382 / % possible obs: 96.8 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 5.9 % / Biso Wilson estimate: 55.3 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.6→2.64 Å / Rmerge(I) obs: 0.57 / % possible all: 93 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3U1N Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 12.218 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 1.172 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.699 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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