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- PDB-6a45: Structure of mouse TREX2 -

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Basic information

Entry
Database: PDB / ID: 6a45
TitleStructure of mouse TREX2
ComponentsThree prime repair exonuclease 2
KeywordsDNA BINDING PROTEIN / Exonuclease / DEDDh exonuclease
Function / homology
Function and homology information


exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / 3'-5'-DNA exonuclease activity / DNA catabolic process / DNA metabolic process / nucleic acid binding / DNA repair / magnesium ion binding / protein homodimerization activity / nucleus / cytoplasm
Similarity search - Function
Three-prime repair exonuclease 1/2 / Exonuclease / 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
PHOSPHATE ION / Three prime repair exonuclease 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.904 Å
AuthorsHsiao, Y.Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
MOST 106-2311-B-009-002 Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural insights into the duplex DNA processing of TREX2
Authors: Cheng, H.L. / Lin, C.T. / Huang, K.W. / Wang, S. / Lin, Y.T. / Toh, S.I. / Hsiao, Y.Y.
History
DepositionJun 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Three prime repair exonuclease 2
B: Three prime repair exonuclease 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5044
Polymers56,3142
Non-polymers1902
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-17 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.293, 54.725, 88.156
Angle α, β, γ (deg.)90.00, 100.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Three prime repair exonuclease 2 / 3'-5' exonuclease TREX2


Mass: 28156.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trex2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9R1A9, exodeoxyribonuclease III
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 1.86 Å3/Da / Density % sol: 34.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES sodium pH 7.5, 0.8M Sodium phosphate monobasic monohydrate, 0.8M Potassium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 32343 / % possible obs: 99.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.039 / Rrim(I) all: 0.078 / Rsym value: 0.078 / Net I/σ(I): 18.85
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 1.76 / Num. unique obs: 3127 / CC1/2: 0.776 / Rpim(I) all: 0.246 / Rrim(I) all: 0.458 / Rsym value: 0.458 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y97

1y97


Resolution: 1.904→26.427 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 21.12
RfactorNum. reflection% reflection
Rfree0.2197 2493 7.71 %
Rwork0.1829 --
obs0.1857 32316 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.904→26.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 10 196 3560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063445
X-RAY DIFFRACTIONf_angle_d0.994680
X-RAY DIFFRACTIONf_dihedral_angle_d12.8781255
X-RAY DIFFRACTIONf_chiral_restr0.034520
X-RAY DIFFRACTIONf_plane_restr0.004612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9043-1.94090.30291240.26541521X-RAY DIFFRACTION91
1.9409-1.98050.25651220.25521623X-RAY DIFFRACTION98
1.9805-2.02350.22761570.21931660X-RAY DIFFRACTION99
2.0235-2.07060.25561390.20011651X-RAY DIFFRACTION99
2.0706-2.12230.23861560.20631666X-RAY DIFFRACTION100
2.1223-2.17970.25421370.19791628X-RAY DIFFRACTION100
2.1797-2.24380.23871210.21674X-RAY DIFFRACTION100
2.2438-2.31620.24351390.20461675X-RAY DIFFRACTION99
2.3162-2.39890.221330.19021645X-RAY DIFFRACTION100
2.3989-2.49490.20081450.18441659X-RAY DIFFRACTION99
2.4949-2.60840.19861290.18271708X-RAY DIFFRACTION100
2.6084-2.74570.22241460.1881617X-RAY DIFFRACTION99
2.7457-2.91760.25221400.19191672X-RAY DIFFRACTION100
2.9176-3.14250.23861290.19421688X-RAY DIFFRACTION100
3.1425-3.45810.21951410.18231664X-RAY DIFFRACTION99
3.4581-3.95710.19911630.16361657X-RAY DIFFRACTION99
3.9571-4.98010.19961230.14321700X-RAY DIFFRACTION99
4.9801-26.430.19981490.17751715X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 7.0123 Å / Origin y: -0.0479 Å / Origin z: 21.2482 Å
111213212223313233
T0.1446 Å20.0076 Å20.0222 Å2-0.1188 Å2-0 Å2--0.1553 Å2
L1.2705 °2-0.2232 °20.2671 °2-1.1224 °2-0.5551 °2--1.7933 °2
S-0.0536 Å °-0.0334 Å °-0.0567 Å °0.191 Å °0.0487 Å °0.0239 Å °0.0193 Å °-0.0319 Å °0.0104 Å °
Refinement TLS groupSelection details: all

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