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- PDB-6a47: Structure of TREX2 in complex with a Y structured dsDNA -

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Basic information

Entry
Database: PDB / ID: 6a47
TitleStructure of TREX2 in complex with a Y structured dsDNA
Components
  • DNA (5'-D(P*CP*CP*AP*GP*GP*CP*CP*CP*TP*CP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
  • Three 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 metabolic process / molecular adaptor activity / DNA repair / magnesium ion binding / protein homodimerization activity / DNA binding / 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
DNA / DNA (> 10) / Three prime repair exonuclease 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Three prime repair exonuclease 2
B: Three prime repair exonuclease 2
C: DNA (5'-D(P*CP*CP*AP*GP*GP*CP*CP*CP*TP*CP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
D: DNA (5'-D(P*CP*CP*AP*GP*GP*CP*CP*CP*TP*CP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4339
Polymers70,3134
Non-polymers1205
Water5,657314
1
A: Three prime repair exonuclease 2
C: DNA (5'-D(P*CP*CP*AP*GP*GP*CP*CP*CP*TP*CP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2285
Polymers35,1562
Non-polymers723
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-36 kcal/mol
Surface area13780 Å2
MethodPISA
2
B: Three prime repair exonuclease 2
D: DNA (5'-D(P*CP*CP*AP*GP*GP*CP*CP*CP*TP*CP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2054
Polymers35,1562
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-23 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.666, 48.404, 90.593
Angle α, β, γ (deg.)90.00, 97.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-553-

HOH

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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: DNA chain DNA (5'-D(P*CP*CP*AP*GP*GP*CP*CP*CP*TP*CP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')


Mass: 6999.495 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Sodium citrate tribasic dihydrate pH 5.0, 30%(v/v) Polyethylene glycol monomethyl ether 550, D-(+)-Glucose monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 4, 2016
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: 50026 / % possible obs: 99.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.024 / Rsym value: 0.05 / Net I/σ(I): 33.34
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.77 / Num. unique obs: 4963 / Rpim(I) all: 0.274 / Rsym value: 0.531 / % possible all: 99.6

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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: 1.9→28.454 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.93
RfactorNum. reflection% reflection
Rfree0.1911 3750 7.55 %
Rwork0.1632 --
obs0.1653 49670 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3430 769 5 314 4518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064371
X-RAY DIFFRACTIONf_angle_d0.9566086
X-RAY DIFFRACTIONf_dihedral_angle_d19.0391657
X-RAY DIFFRACTIONf_chiral_restr0.037683
X-RAY DIFFRACTIONf_plane_restr0.005667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9240.31481450.26821686X-RAY DIFFRACTION99
1.924-1.94940.27331290.24041653X-RAY DIFFRACTION100
1.9494-1.97610.25271340.22141714X-RAY DIFFRACTION100
1.9761-2.00430.26451060.211698X-RAY DIFFRACTION100
2.0043-2.03420.23841400.2011692X-RAY DIFFRACTION100
2.0342-2.0660.25671370.19141673X-RAY DIFFRACTION100
2.066-2.09980.21691550.19541712X-RAY DIFFRACTION100
2.0998-2.1360.23321420.18241687X-RAY DIFFRACTION100
2.136-2.17480.20881190.17671684X-RAY DIFFRACTION100
2.1748-2.21670.22121410.17871672X-RAY DIFFRACTION100
2.2167-2.26190.22011510.18251659X-RAY DIFFRACTION100
2.2619-2.31110.21551370.1651734X-RAY DIFFRACTION100
2.3111-2.36480.21251270.15911677X-RAY DIFFRACTION100
2.3648-2.42390.18681610.16051684X-RAY DIFFRACTION100
2.4239-2.48940.1991460.16941666X-RAY DIFFRACTION100
2.4894-2.56260.21011530.16561725X-RAY DIFFRACTION100
2.5626-2.64530.20081290.16661703X-RAY DIFFRACTION100
2.6453-2.73970.20991300.17011696X-RAY DIFFRACTION100
2.7397-2.84930.17541370.17141744X-RAY DIFFRACTION100
2.8493-2.97890.21971420.17521662X-RAY DIFFRACTION100
2.9789-3.13570.23171440.18511703X-RAY DIFFRACTION100
3.1357-3.33190.21631360.16831711X-RAY DIFFRACTION100
3.3319-3.58870.18191370.16461709X-RAY DIFFRACTION100
3.5887-3.9490.17121520.14591720X-RAY DIFFRACTION100
3.949-4.51850.14561510.12261721X-RAY DIFFRACTION100
4.5185-5.68540.15681370.14051739X-RAY DIFFRACTION100
5.6854-28.45690.15741320.15741796X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 11.1356 Å / Origin y: -25.8473 Å / Origin z: -20.3281 Å
111213212223313233
T0.1983 Å2-0.0274 Å20.0186 Å2-0.1171 Å2-0.0042 Å2--0.1745 Å2
L1.4861 °2-0.0893 °20.3233 °2-0.9421 °2-0.0444 °2--1.8761 °2
S0.0198 Å °-0.0584 Å °-0.0328 Å °-0.0085 Å °0.0285 Å °-0.0491 Å °0.0858 Å °-0.1404 Å °-0.0411 Å °
Refinement TLS groupSelection details: all

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