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Yorodumi- PDB-3b6o: Structure of TREX1 in complex with a nucleotide and an inhibitor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b6o | ||||||
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Title | Structure of TREX1 in complex with a nucleotide and an inhibitor ion (lithium) | ||||||
Components | Three prime repair exonuclease 1 | ||||||
Keywords | HYDROLASE / TREX1 / DEDD / exonuclease / DnaQ / lithium / catalysis / inhibition / deoxy-thimidine monophosphate (dTMP) / DNA damage / DNA repair / Magnesium / Nucleus / Phosphorylation | ||||||
Function / homology | Function and homology information immune response in brain or nervous system / adenyl deoxyribonucleotide binding / CD86 biosynthetic process / immune complex formation / cellular response to type I interferon / organ or tissue specific immune response / atrial cardiac muscle tissue development / activation of immune response / DNA synthesis involved in UV-damage excision repair / T cell antigen processing and presentation ...immune response in brain or nervous system / adenyl deoxyribonucleotide binding / CD86 biosynthetic process / immune complex formation / cellular response to type I interferon / organ or tissue specific immune response / atrial cardiac muscle tissue development / activation of immune response / DNA synthesis involved in UV-damage excision repair / T cell antigen processing and presentation / MutSalpha complex binding / retrotransposition / oligosaccharyltransferase complex / regulation of lysosome organization / DNA modification / regulation of lipid biosynthetic process / WW domain binding / regulation of fatty acid metabolic process / heart process / regulation of protein complex stability / MutLalpha complex binding / cellular response to hydroxyurea / lymphoid progenitor cell differentiation / double-stranded DNA 3'-5' DNA exonuclease activity / regulation of type I interferon production / exodeoxyribonuclease III / macrophage activation involved in immune response / regulation of tumor necrosis factor production / regulation of cellular respiration / inflammatory response to antigenic stimulus / DNA catabolic process / regulation of immunoglobulin production / apoptotic cell clearance / regulation of T cell activation / regulation of glycolytic process / DNA binding, bending / DNA duplex unwinding / 3'-5'-DNA exonuclease activity / DNA metabolic process / negative regulation of type I interferon-mediated signaling pathway / : / negative regulation of cGAS/STING signaling pathway / type I interferon-mediated signaling pathway / regulation of innate immune response / blood vessel development / mitotic G1 DNA damage checkpoint signaling / nuclear replication fork / cellular response to interferon-beta / generation of precursor metabolites and energy / heart morphogenesis / response to UV / 3'-5' exonuclease activity / negative regulation of innate immune response / DNA damage checkpoint signaling / kidney development / determination of adult lifespan / protein-DNA complex / cellular response to reactive oxygen species / establishment of protein localization / cellular response to gamma radiation / cellular response to UV / regulation of inflammatory response / double-stranded DNA binding / regulation of gene expression / single-stranded DNA binding / cellular response to oxidative stress / DNA replication / defense response to virus / adaptive immune response / protein stabilization / inflammatory response / immune response / innate immune response / DNA damage response / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / DNA binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Brucet, M. / Querol-Audi, J. / Fita, I. / Celada, A. | ||||||
Citation | Journal: Protein Sci. / Year: 2008 Title: Structural and biochemical studies of TREX1 inhibition by metals. Identification of a new active histidine conserved in DEDDh exonucleases. Authors: Brucet, M. / Querol-Audi, J. / Bertlik, K. / Lloberas, J. / Fita, I. / Celada, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b6o.cif.gz | 187.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b6o.ent.gz | 147.7 KB | Display | PDB format |
PDBx/mmJSON format | 3b6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/3b6o ftp://data.pdbj.org/pub/pdb/validation_reports/b6/3b6o | HTTPS FTP |
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-Related structure data
Related structure data | 3b6pC 2o4gS 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: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 5 / Auth seq-ID: 9 - 234 / Label seq-ID: 11 - 236
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-Components
#1: Protein | Mass: 27173.010 Da / Num. of mol.: 4 / Fragment: TREX1 exonuclease, UNP residues 9-245 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trex1 / Plasmid: pETM-10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q91XB0, exodeoxyribonuclease III #2: Chemical | ChemComp-LI / #3: Chemical | ChemComp-TMP / #4: 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: 2.25 Å3/Da / Density % sol: 45.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 22% PEG3350, 100 mM MES pH 6.0, 200 mM Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 65149 / Num. obs: 65149 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.106 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.514 / % possible all: 75.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 2o4g Resolution: 2.1→24.67 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.923 / SU B: 11.689 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 31.667 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→24.67 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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