+Open data
-Basic information
Entry | Database: PDB / ID: 3mxi | ||||||
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Title | TREX1 3' Exonuclease D18N Familial Chilblain Lupus Mutant | ||||||
Components |
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Keywords | HYDROLASE/DNA / RNase H-like fold / Polyproline type II helix / HYDROLASE-DNA complex | ||||||
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 / regulation of fatty acid metabolic process / regulation of lipid biosynthetic process / DNA modification / MutLalpha complex binding / WW domain binding / regulation of type I interferon production / heart process / regulation of protein complex stability / cellular response to hydroxyurea / lymphoid progenitor cell differentiation / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / 3'-5'-DNA exonuclease activity / macrophage activation involved in immune response / regulation of tumor necrosis factor production / regulation of cellular respiration / regulation of immunoglobulin production / inflammatory response to antigenic stimulus / DNA catabolic process / apoptotic cell clearance / regulation of T cell activation / DNA binding, bending / DNA duplex unwinding / regulation of glycolytic process / DNA metabolic process / negative regulation of type I interferon-mediated signaling pathway / cellular response to organic substance / regulation of innate immune response / negative regulation of cGAS/STING signaling pathway / type I interferon-mediated signaling pathway / blood vessel development / nuclear replication fork / cellular response to interferon-beta / heart morphogenesis / response to UV / 3'-5' exonuclease activity / mitotic G1 DNA damage checkpoint signaling / negative regulation of innate immune response / kidney development / generation of precursor metabolites and energy / DNA damage checkpoint signaling / determination of adult lifespan / protein-DNA complex / establishment of protein localization / cellular response to gamma radiation / cellular response to reactive oxygen species / cellular response to UV / single-stranded DNA binding / cellular response to oxidative stress / regulation of inflammatory response / double-stranded DNA binding / regulation of gene expression / defense response to virus / adaptive immune response / DNA replication / protein stabilization / immune response / inflammatory response / innate immune response / DNA damage response / endoplasmic reticulum membrane / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / DNA binding / nucleus / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Bailey, S.L. / Hollis, T. | ||||||
Citation | Journal: To be Published Title: X-ray Crystal Structures of TREX1 3' Exonuclease Autoimmune Disease Mutants Authors: Bailey, S.L. / Harvey, S. / Perrino, F.W. / Hollis, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mxi.cif.gz | 102.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mxi.ent.gz | 76.9 KB | Display | PDB format |
PDBx/mmJSON format | 3mxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/3mxi ftp://data.pdbj.org/pub/pdb/validation_reports/mx/3mxi | HTTPS FTP |
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-Related structure data
Related structure data | 3mxjC 3mxmC 3mxk 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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-Components
#1: Protein | Mass: 26322.977 Da / Num. of mol.: 2 / Fragment: N-terminal fragment, residues 1-242 / Mutation: D18N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trex1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91XB0, exodeoxyribonuclease III #2: DNA chain | Mass: 1215.843 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.28 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.15 M MES pH 6.5 19% PEG 4000 10% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→42.78 Å / Num. all: 15296 / Num. obs: 14777 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 26.92 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 6.54 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4.5 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→31.476 Å / SU ML: 0.39 / σ(F): 1.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.55→31.476 Å
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Refine LS restraints |
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LS refinement shell |
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