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- PDB-6a4b: Structure of TREX2 in complex with a duplex DNA with 2 nucleotide... -

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Basic information

Entry
Database: PDB / ID: 6a4b
TitleStructure of TREX2 in complex with a duplex DNA with 2 nucleotide 3'-overhang
Components
  • DNA (5'-D(*GP*GP*CP*CP*CP*TP*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


double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / 3'-5'-DNA exonuclease activity / DNA metabolic process / nucleic acid binding / DNA repair / magnesium ion binding / protein homodimerization activity / nucleus
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: 2.7 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: Three prime repair exonuclease 2
D: Three prime repair exonuclease 2
E: Three prime repair exonuclease 2
F: Three prime repair exonuclease 2
G: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
H: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
I: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
J: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
K: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
L: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,05623
Polymers201,78812
Non-polymers26711
Water57632
1
A: Three prime repair exonuclease 2
B: Three prime repair exonuclease 2
G: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
H: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3608
Polymers67,2634
Non-polymers974
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-45 kcal/mol
Surface area22720 Å2
MethodPISA
2
C: Three prime repair exonuclease 2
D: Three prime repair exonuclease 2
I: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
J: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3367
Polymers67,2634
Non-polymers733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-33 kcal/mol
Surface area23670 Å2
MethodPISA
3
E: Three prime repair exonuclease 2
F: Three prime repair exonuclease 2
K: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
L: DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3608
Polymers67,2634
Non-polymers974
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-41 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.715, 87.317, 432.941
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 2 / 3'-5' exonuclease TREX2


Mass: 28156.832 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trex2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9R1A9, exodeoxyribonuclease III
#2: DNA chain
DNA (5'-D(*GP*GP*CP*CP*CP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')


Mass: 5474.526 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Sodium citrate tribasic dihydrate pH 5.5, 22%(w/v) Polyethylene glycol 1,000, 0.1M Barium chloride dihydrate

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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: May 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 51078 / % possible obs: 97.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.04 / Rsym value: 0.078 / Net I/σ(I): 23.45
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 1.93 / Num. unique obs: 4998 / Rpim(I) all: 0.31 / Rsym value: 0.581 / % possible all: 97.1

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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: 2.7→29.233 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2632 3961 7.8 %
Rwork0.2243 --
obs0.2274 50754 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→29.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10082 1857 11 32 11982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312397
X-RAY DIFFRACTIONf_angle_d0.68717200
X-RAY DIFFRACTIONf_dihedral_angle_d17.4534658
X-RAY DIFFRACTIONf_chiral_restr0.0251932
X-RAY DIFFRACTIONf_plane_restr0.0031928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.73290.38991370.34551600X-RAY DIFFRACTION97
2.7329-2.76750.34721380.35531610X-RAY DIFFRACTION97
2.7675-2.80390.37121530.34111630X-RAY DIFFRACTION98
2.8039-2.84220.39021580.32811697X-RAY DIFFRACTION98
2.8422-2.88280.36111350.3171655X-RAY DIFFRACTION98
2.8828-2.92580.36261530.30731624X-RAY DIFFRACTION97
2.9258-2.97150.33741340.31191644X-RAY DIFFRACTION98
2.9715-3.02010.32511360.30011716X-RAY DIFFRACTION99
3.0201-3.07220.29441310.2981643X-RAY DIFFRACTION98
3.0722-3.1280.34211500.27731684X-RAY DIFFRACTION98
3.128-3.18810.30361520.27471646X-RAY DIFFRACTION99
3.1881-3.25310.31511400.26771718X-RAY DIFFRACTION99
3.2531-3.32370.30351280.26631644X-RAY DIFFRACTION98
3.3237-3.40090.31711400.26811665X-RAY DIFFRACTION98
3.4009-3.48580.28431400.25131720X-RAY DIFFRACTION98
3.4858-3.57990.28491360.23151629X-RAY DIFFRACTION98
3.5799-3.6850.27391380.23681688X-RAY DIFFRACTION98
3.685-3.80370.26931440.24021686X-RAY DIFFRACTION98
3.8037-3.93940.27181370.22211661X-RAY DIFFRACTION98
3.9394-4.09670.27591080.21051714X-RAY DIFFRACTION97
4.0967-4.28260.2151370.2071660X-RAY DIFFRACTION98
4.2826-4.50760.24941350.19181707X-RAY DIFFRACTION97
4.5076-4.78890.22681530.19081681X-RAY DIFFRACTION97
4.7889-5.15680.25871460.18831692X-RAY DIFFRACTION97
5.1568-5.67230.26661430.19681734X-RAY DIFFRACTION98
5.6723-6.48530.26071620.21031717X-RAY DIFFRACTION98
6.4853-8.14150.19731560.19271771X-RAY DIFFRACTION97
8.1415-29.23460.21621410.18651557X-RAY DIFFRACTION82
Refinement TLS params.Method: refined / Origin x: -13.6746 Å / Origin y: -23.6668 Å / Origin z: -54.2933 Å
111213212223313233
T0.4339 Å2-0.0245 Å2-0.0192 Å2-0.5228 Å2-0.0779 Å2--0.5538 Å2
L0.395 °2-0.3087 °2-0.2222 °2-1.1214 °20.829 °2--1.3646 °2
S-0.0277 Å °0.1822 Å °-0.0045 Å °0.1369 Å °-0.0188 Å °-0.0682 Å °-0.1318 Å °-0.012 Å °0.0479 Å °
Refinement TLS groupSelection details: all

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