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- PDB-3mxj: Crystal Structure of the mTREX1 Apoprotein -

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Basic information

Entry
Database: PDB / ID: 3mxj
TitleCrystal Structure of the mTREX1 Apoprotein
ComponentsThree prime repair exonuclease 1
KeywordsHYDROLASE / RNase H-like fold / Polyproline II helix
Function / homology
Function and homology information


immune response in brain or nervous system / T cell antigen processing and presentation / immune complex formation / organ or tissue specific immune response / adenyl deoxyribonucleotide binding / activation of immune response / DNA synthesis involved in UV-damage excision repair / atrial cardiac muscle tissue development / lymphoid progenitor cell differentiation / retrotransposition ...immune response in brain or nervous system / T cell antigen processing and presentation / immune complex formation / organ or tissue specific immune response / adenyl deoxyribonucleotide binding / activation of immune response / DNA synthesis involved in UV-damage excision repair / atrial cardiac muscle tissue development / lymphoid progenitor cell differentiation / retrotransposition / DNA exonuclease activity / regulation of catalytic activity / MutSalpha complex binding / DNA modification / regulation of immunoglobulin production / cellular response to hydroxyurea / regulation of lipid biosynthetic process / oligosaccharyltransferase complex / regulation of lysosome organization / regulation of cellular respiration / regulation of fatty acid metabolic process / regulation of protein complex stability / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / regulation of type I interferon production / inflammatory response to antigenic stimulus / regulation of tumor necrosis factor production / regulation of T cell activation / 3'-5'-DNA exonuclease activity / heart process / macrophage activation involved in immune response / blood vessel development / MutLalpha complex binding / glycoprotein biosynthetic process / DNA catabolic process / apoptotic cell clearance / negative regulation of type I interferon-mediated signaling pathway / regulation of glycolytic process / DNA binding, bending / DNA metabolic process / type I interferon-mediated signaling pathway / WW domain binding / cGAS/STING signaling pathway / regulation of innate immune response / cellular response to type I interferon / negative regulation of cGAS/STING signaling pathway / response to UV / nuclear replication fork / heart morphogenesis / determination of adult lifespan / cellular response to interferon-beta / DNA damage checkpoint signaling / kidney development / mitotic G1 DNA damage checkpoint signaling / 3'-5' exonuclease activity / negative regulation of innate immune response / generation of precursor metabolites and energy / establishment of protein localization / cellular response to reactive oxygen species / cellular response to gamma radiation / protein-DNA complex / cellular response to UV / regulation of gene expression / adaptive immune response / single-stranded DNA binding / regulation of inflammatory response / defense response to virus / cellular response to oxidative stress / double-stranded DNA binding / DNA replication / innate immune response / protein stabilization / inflammatory response / immune response / DNA damage response / endoplasmic reticulum membrane / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / DNA binding / identical protein binding / nucleus / 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
Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)52,6482
Polymers52,6482
Non-polymers00
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-0 kcal/mol
Surface area17570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.160, 85.720, 100.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 26323.961 Da / Num. of mol.: 2 / Fragment: N-terminal fragment, residues 1-242
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.25 M tri-sodium citrate dihydrate 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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: 1.95→29 Å / Num. obs: 40918 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.72 % / Biso Wilson estimate: 24.71 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 16
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.63 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 4.1 / % possible all: 97.1

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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: 1.95→28.781 Å / SU ML: 0.27 / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 2044 5.03 %Random
Rwork0.2038 ---
obs0.2055 40666 99.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.365 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.1263 Å2-0 Å2-0 Å2
2---0.8299 Å20 Å2
3----5.2964 Å2
Refinement stepCycle: LAST / Resolution: 1.95→28.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3311 0 0 242 3553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073393
X-RAY DIFFRACTIONf_angle_d1.054623
X-RAY DIFFRACTIONf_dihedral_angle_d15.6081260
X-RAY DIFFRACTIONf_chiral_restr0.068528
X-RAY DIFFRACTIONf_plane_restr0.005601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.01970.2721860.21063702X-RAY DIFFRACTION97
2.0197-2.10050.27592090.19633820X-RAY DIFFRACTION100
2.1005-2.19610.23692200.19623841X-RAY DIFFRACTION100
2.1961-2.31180.35411810.31453720X-RAY DIFFRACTION96
2.3118-2.45660.24891870.20513884X-RAY DIFFRACTION100
2.4566-2.64620.25411950.1983872X-RAY DIFFRACTION100
2.6462-2.91220.26271920.22023908X-RAY DIFFRACTION100
2.9122-3.33310.26682120.21013900X-RAY DIFFRACTION100
3.3331-4.19730.19222130.17553913X-RAY DIFFRACTION100
4.1973-28.78380.19172490.17234062X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.031.0377-1.87221.188-0.82841.94110.23080.2040.1350.1121-0.08270.1223-0.3239-0.1767-0.1620.13640.00280.03990.1004-0.00540.1258-6.30995.023636.2964
20.4977-0.72280.410.7979-0.28271.4199-0.04950.2510.22380.0358-0.0267-0.0646-0.02980.15360.07140.1079-0.0095-0.01010.1141-0.00350.15238.61113.154930.7256
30.06910.2871-0.43375.2762-2.40762.10640.2538-0.5505-0.2152-0.18970.35060.9520.1727-0.4377-0.46740.1621-0.1564-0.06460.34230.06360.2975-12.5892-8.754432.0146
41.19620.64950.22330.799-0.73341.67740.00010.2317-0.01820.02260.0222-0.1490.11760.1422-0.0030.08920.01250.00550.1183-0.02390.13493.4660.45423.2287
52.35261.76062.13611.49171.22713.07420.54780.0437-0.4872-0.01710.0155-0.58590.5330.0224-0.46670.41730.114-0.06350.33780.04470.420819.9476-5.826928.3604
63.9826-1.82411.04470.9274-0.3090.57260.07180.6843-0.2596-0.1305-0.18480.21480.09760.27740.09490.2002-0.0221-0.01890.3390.01370.197917.96273.879917.76
70.2987-0.0789-0.35320.2107-0.25031.28290.06110.01060.01950.194-0.0698-0.0157-0.2671-0.05990.0160.1654-0.0172-0.01950.14410.00420.1685-0.0749.652528.2866
80.30580.8344-0.42662.9408-1.91361.78950.11130.0447-0.05170.2006-0.0134-0.0004-0.16490.3031-0.07530.1075-0.0413-0.00840.1561-0.00920.15779.107611.916133.2942
91.25340.11370.20682.43440.65230.2801-0.0144-0.18220.16360.41750.06250.07730.0125-0.0006-0.00840.161-0.01540.00090.1701-0.00780.1453-1.2822.257140.709
100.2978-0.0780.34320.841-0.70490.66050.04540.0131-0.07670.0266-0.0572-0.17690.04260.02810.01480.1996-0.0149-0.01020.13920.0130.17561.0837-15.279138.6684
112.62230.6709-2.6050.2592-0.55262.9483-0.2608-0.0841-0.4219-0.1432-0.0511-0.08380.37730.08990.23350.1728-0.0083-0.01180.13840.02060.1913-0.3098-7.787930.7085
120.0372-0.0867-0.02050.3894-0.05661.313-0.0144-0.0474-0.07120.12340.0858-0.0276-0.0595-0.4507-0.05040.17430.01030.0510.26640.0080.2074-9.6225-1.28242.5109
133.89721.4654-1.27222.27660.14631.3551-0.0434-0.66270.05710.5010.0447-0.0246-0.15740.354-0.0330.211-0.0224-0.03210.2163-0.03750.20157.45411.75340.2546
142.7311-0.0071-1.86781.77510.10211.6729-0.0940.2182-0.1341-0.37030.1303-0.15090.10660.0171-0.04880.2094-0.04440.06430.219-0.00520.15717.5023.49810.3743
151.6286-1.15060.74390.9523-0.40221.21040.1721-0.08650.1277-0.1893-0.0858-0.00150.1228-0.1875-0.06610.1445-0.018-0.04440.1917-0.00260.158-10.28882.31568.3683
160.5729-0.3466-0.56093.1462-3.31865.1241-0.1629-0.55190.1328-0.1179-0.0891-1.24590.33240.57690.24760.16290.05860.04150.33490.00870.295715.6939-3.41316.6624
171.7077-0.3041-2.53840.21430.77044.8014-0.60990.2108-0.20220.8522-0.1611-0.79730.6501-0.10320.68580.42380.0672-0.10170.13750.04060.66829.2726-18.10678.1817
180.0978-0.4950.2441.7715-0.31732.09820.136-0.2285-0.4453-0.13610.06760.44750.2588-0.5563-0.1860.1427-0.0653-0.05590.24380.04960.2315-9.9788-1.004314.7265
190.17240.67520.37334.8771-2.0276.890.0963-0.2097-0.03580.07260.06160.62220.2478-1.2118-0.17150.12080.0476-0.02320.41790.01650.2096-17.14146.102720.535
201.2308-0.2262-0.57250.05370.30431.38740.04030.0270.0833-0.0968-0.0281-0.0288-0.30220.0483-0.01050.1441-0.0016-0.00530.11590.00840.13032.339610.594811.3064
210.3754-0.33550.2741.9190.5980.78590.01310.0751-0.0453-0.2944-0.10490.2106-0.073-0.20880.09160.1705-0.0207-0.0330.2185-0.01530.1692-8.60193.56581.4237
228.8326-5.8861-4.18444.04533.18753.87820.403-0.04820.6302-0.3657-0.1293-0.4023-0.6539-0.2234-0.17720.21010.039-0.04450.12170.01080.1349-6.924416.92367.7435
231.08270.728-0.19610.3244-0.0480.02720.0490.263-0.0426-0.0787-0.0160.04770.0183-0.01-0.0140.2148-0.01350.01740.2277-0.05830.18661.1861-4.4678-3.6103
240.91520.2142-1.10010.8306-1.39613.3861-0.3061-0.01210.1085-0.23180.0883-0.54820.82430.04330.09360.3677-0.0661-0.01460.137-0.05990.2973-2.751-16.38625.2361
251.3172-0.3128-0.68530.71870.61852.565-0.15380.1017-0.1861-0.1634-0.01-0.16940.31220.02140.16110.17650.00450.03120.1678-0.01370.18444.5947-5.63592.386
262.4474-0.65051.19871.0545-0.15440.6813-0.0190.21730.1542-0.28980.05020.1391-0.2113-0.2624-0.02620.18510.027-0.02690.2440.04310.1501-8.448310.4672-1.8213
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 6:19)
2X-RAY DIFFRACTION2(chain A and resid 20:41)
3X-RAY DIFFRACTION3(chain A and resid 42:58)
4X-RAY DIFFRACTION4(chain A and resid 59:77)
5X-RAY DIFFRACTION5(chain A and resid 78:86)
6X-RAY DIFFRACTION6(chain A and resid 87:99)
7X-RAY DIFFRACTION7(chain A and resid 100:127)
8X-RAY DIFFRACTION8(chain A and resid 128:146)
9X-RAY DIFFRACTION9(chain A and resid 147:162)
10X-RAY DIFFRACTION10(chain A and resid 163:192)
11X-RAY DIFFRACTION11(chain A and resid 194:210)
12X-RAY DIFFRACTION12(chain A and resid 211:223)
13X-RAY DIFFRACTION13(chain A and resid 224:234)
14X-RAY DIFFRACTION14(chain B and resid 4:19)
15X-RAY DIFFRACTION15(chain B and resid 20:40)
16X-RAY DIFFRACTION16(chain B and resid 41:46)
17X-RAY DIFFRACTION17(chain B and resid 47:59)
18X-RAY DIFFRACTION18(chain B and resid 60:88)
19X-RAY DIFFRACTION19(chain B and resid 89:100)
20X-RAY DIFFRACTION20(chain B and resid 101:122)
21X-RAY DIFFRACTION21(chain B and resid 123:137)
22X-RAY DIFFRACTION22(chain B and resid 138:147)
23X-RAY DIFFRACTION23(chain B and resid 148:176)
24X-RAY DIFFRACTION24(chain B and resid 177:195)
25X-RAY DIFFRACTION25(chain B and resid 196:224)
26X-RAY DIFFRACTION26(chain B and resid 225:234)

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