+Open data
-Basic information
Entry | Database: PDB / ID: 4rxr | ||||||
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Title | The structure of GTP-dCTP-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: 2.117 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 | 4rxr.cif.gz | 225.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rxr.ent.gz | 176.5 KB | Display | PDB format |
PDBx/mmJSON format | 4rxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/4rxr ftp://data.pdbj.org/pub/pdb/validation_reports/rx/4rxr | HTTPS FTP |
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-Related structure data
Related structure data | 4rxoC 4rxpC 4rxqC 4rxsC 4mz7S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: _ / Auth seq-ID: 114 - 598 / Label seq-ID: 27 - 511
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-Components
#1: Protein | Mass: 62486.184 Da / Num. of mol.: 2 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-DCP / #3: Chemical | #4: Chemical | #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: 2.54 Å3/Da / Density % sol: 51.61 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M lithium sulfate monohydrate, 0.1M sodium citrate tribasic dihydrate, and 20% w/v polyethylene glycol 1000 , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 7, 2014 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 70499 / Num. obs: 70217 / % possible obs: 99.6 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 6.9 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 39.4 |
Reflection shell | Resolution: 2.1→2.14 Å / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 3.9 / % possible all: 99.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MZ7 Resolution: 2.117→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.672 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.2 / ESU R Free: 0.166 / 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: 49.707 Å2
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Refinement step | Cycle: LAST / Resolution: 2.117→50 Å
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