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Yorodumi- PDB-4mz7: Structural insight into dGTP-dependent activation of tetrameric S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mz7 | ||||||
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Title | Structural insight into dGTP-dependent activation of tetrameric SAMHD1 deoxynucleoside triphosphate triphosphohydrolase | ||||||
Components | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | ||||||
Keywords | HYDROLASE / HD-domain / dNTP Binding / Phosphorylation | ||||||
Function / homology | Function and homology information Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / triphosphoric monoester hydrolase activity / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / dGTP catabolic process / DNA strand resection involved in replication fork processing ...Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / triphosphoric monoester hydrolase activity / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / dGTP catabolic process / DNA strand resection involved in replication fork processing / deoxyribonucleotide catabolic process / regulation of innate immune response / negative regulation of type I interferon-mediated signaling pathway / somatic hypermutation of immunoglobulin genes / RNA nuclease activity / double-strand break repair via homologous recombination / Interferon alpha/beta signaling / single-stranded DNA binding / site of double-strand break / 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: 1.8 Å | ||||||
Authors | Zhu, C. / Gao, W. / Zhao, K. / Qin, X. / Zhang, Y. / Peng, X. / Zhang, L. / Dong, Y. / Zhang, W. / Li, P. ...Zhu, C. / Gao, W. / Zhao, K. / Qin, X. / Zhang, Y. / Peng, X. / Zhang, L. / Dong, Y. / Zhang, W. / Li, P. / Wei, W. / Gong, Y. / Yu, X.F. | ||||||
Citation | Journal: Nat Commun / Year: 2013 Title: Structural insight into dGTP-dependent activation of tetrameric SAMHD1 deoxynucleoside triphosphate triphosphohydrolase Authors: Zhu, C. / Gao, W. / Zhao, K. / Qin, X. / Zhang, Y. / Peng, X. / Zhang, L. / Dong, Y. / Zhang, W. / Li, P. / Wei, W. / 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 | 4mz7.cif.gz | 239 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mz7.ent.gz | 186.8 KB | Display | PDB format |
PDBx/mmJSON format | 4mz7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/4mz7 ftp://data.pdbj.org/pub/pdb/validation_reports/mz/4mz7 | HTTPS FTP |
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-Related structure data
Related structure data | 3u1nS S: Starting model for refinement |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 62486.184 Da / Num. of mol.: 2 / Fragment: UNP residues 109-626 / Mutation: C266Y 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 |
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-Non-polymers , 5 types, 829 molecules
#2: Chemical | #3: Chemical | ChemComp-DGT / #4: Chemical | #5: Chemical | ChemComp-DTP / | #6: 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: 2.39 Å3/Da / Density % sol: 48.48 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M MES (pH 6.5), 25%(w/v) polyethylene glycol monomethyle ether 550, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 19, 2013 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 108184 / % possible obs: 100 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 6.4 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 27.2 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3U1N Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.135 / ESU R Free: 0.125 / 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: 22.609 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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