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Yorodumi- PDB-4tnp: Structural basis of cellular dNTP regulation, SAMHD1-GTP-dCTP-cCT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tnp | |||||||||
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Title | Structural basis of cellular dNTP regulation, SAMHD1-GTP-dCTP-cCTP complex | |||||||||
Components | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | |||||||||
Keywords | HYDROLASE / SAMHD1 / HIV / restriction factor / dNTPase / dNTP regulation / host pathogen interaction | |||||||||
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 Å | |||||||||
Authors | Ji, X. / Tang, C. / Zhao, Q. / Wang, W. / Xiong, Y. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Structural basis of cellular dNTP regulation by SAMHD1. Authors: Ji, X. / Tang, C. / Zhao, Q. / Wang, W. / Xiong, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tnp.cif.gz | 816.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tnp.ent.gz | 674.6 KB | Display | PDB format |
PDBx/mmJSON format | 4tnp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4tnp_validation.pdf.gz | 4.5 MB | Display | wwPDB validaton report |
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Full document | 4tnp_full_validation.pdf.gz | 4.6 MB | Display | |
Data in XML | 4tnp_validation.xml.gz | 73 KB | Display | |
Data in CIF | 4tnp_validation.cif.gz | 98.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/4tnp ftp://data.pdbj.org/pub/pdb/validation_reports/tn/4tnp | HTTPS FTP |
-Related structure data
Related structure data | 4tnqC 4tnrC 4tnxC 4tnyC 4tnzC 4to0C 4to1C 4to2C 4to3C 4to4C 4to5C 4to6C 4bzbS C: citing same article (ref.) S: Starting model for refinement |
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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: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 59604.172 Da / Num. of mol.: 4 / Fragment: UNP residues 113-626 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 | ChemComp-GTP / #4: Chemical | ChemComp-MG / #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: 2.15 Å3/Da / Density % sol: 42.73 % |
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Crystal grow | Temperature: 298 K / Method: batch mode / pH: 7.4 / Details: SPG buffer, PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 131807 / % possible obs: 98.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.125 / Χ2: 1.029 / Net I/av σ(I): 6.687 / Net I/σ(I): 8.1 / Num. measured all: 419174 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BZB Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 16.661 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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 max: 125.29 Å2 / Biso mean: 32.077 Å2 / Biso min: 13.85 Å2
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Refinement step | Cycle: final / Resolution: 2→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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