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- PDB-3mxi: TREX1 3' Exonuclease D18N Familial Chilblain Lupus Mutant -

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Basic information

Entry
Database: PDB / ID: 3mxi
TitleTREX1 3' Exonuclease D18N Familial Chilblain Lupus Mutant
Components
  • DNA (5'-D(*GP*AP*CP*G)-3')
  • Three prime repair exonuclease 1
KeywordsHYDROLASE/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
Three-prime repair exonuclease 1/2 / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsBailey, S.L. / Hollis, T.
CitationJournal: 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
DepositionMay 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Three prime repair exonuclease 1
A: Three prime repair exonuclease 1
C: DNA (5'-D(*GP*AP*CP*G)-3')
D: DNA (5'-D(*GP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2388
Polymers55,0784
Non-polymers1604
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-63 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.028, 58.776, 66.523
Angle α, β, γ (deg.)90.00, 110.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Three prime repair exonuclease 1 / 3'-5' exonuclease TREX1


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 DNA (5'-D(*GP*AP*CP*G)-3')


Mass: 1215.843 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.55→2.64 Å / Redundancy: 6.54 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4.5 / % possible all: 95.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.4_113)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→31.476 Å / SU ML: 0.39 / σ(F): 1.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.262 767 5.2 %Random
Rwork0.2093 ---
obs0.2121 14747 96.52 %-
Solvent computationShrinkage 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
Baniso -1Baniso -2Baniso -3
1-2.6492 Å20 Å2-9.0118 Å2
2---4.2105 Å2-0 Å2
3---2.9006 Å2
Refinement stepCycle: LAST / Resolution: 2.55→31.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 162 4 93 3589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083594
X-RAY DIFFRACTIONf_angle_d1.284930
X-RAY DIFFRACTIONf_dihedral_angle_d18.5211334
X-RAY DIFFRACTIONf_chiral_restr0.078562
X-RAY DIFFRACTIONf_plane_restr0.006612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.74680.35571580.2492698X-RAY DIFFRACTION95
2.7468-3.0230.29381460.23052763X-RAY DIFFRACTION96
3.023-3.460.25671560.20682799X-RAY DIFFRACTION97
3.46-4.35740.21711490.16822831X-RAY DIFFRACTION97
4.3574-31.47810.22191580.18022889X-RAY DIFFRACTION98

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