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- PDB-6a46: Structure of TREX2 in complex with a nucleotide (dCMP) -

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Basic information

Entry
Database: PDB / ID: 6a46
TitleStructure of TREX2 in complex with a nucleotide (dCMP)
ComponentsThree 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 / molecular adaptor activity / DNA repair / magnesium ion binding / protein homodimerization activity / DNA binding ...: / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / 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
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / Three prime repair exonuclease 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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

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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)57,14611
Polymers56,3142
Non-polymers8329
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-75 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.808, 54.773, 88.716
Angle α, β, γ (deg.)90.00, 100.76, 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DCM / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / Deoxycytidine monophosphate


Mass: 307.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O7P
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 33.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.02M Nickel(II) chloride hexahydrate, 0.02M Magnesium chloride hexahydrate, 0.02M Cadmium chloride hydrate, 0.1M Sodium acetate trihydrate pH 4.5, 24%(w/v) Polyethylene glycol monomethyl ether 2,000

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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 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 27839 / % possible obs: 99.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.033 / Rsym value: 0.061 / Net I/σ(I): 22.37
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 1.875 / Num. unique obs: 2726 / Rpim(I) all: 0.344 / Rsym value: 0.589 / % possible all: 98.1

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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→28.859 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.51
RfactorNum. reflection% reflection
Rfree0.2282 2138 7.69 %
Rwork0.1927 --
obs0.1955 27790 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→28.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3396 0 45 111 3552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033531
X-RAY DIFFRACTIONf_angle_d0.7394806
X-RAY DIFFRACTIONf_dihedral_angle_d11.411280
X-RAY DIFFRACTIONf_chiral_restr0.027533
X-RAY DIFFRACTIONf_plane_restr0.003626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.04660.36961280.31571645X-RAY DIFFRACTION97
2.0466-2.09780.34871340.29811688X-RAY DIFFRACTION97
2.0978-2.15450.27611230.26141694X-RAY DIFFRACTION98
2.1545-2.21790.27561280.25671723X-RAY DIFFRACTION99
2.2179-2.28940.29751380.25961691X-RAY DIFFRACTION98
2.2894-2.37120.26621270.23271696X-RAY DIFFRACTION99
2.3712-2.46610.29781510.22411718X-RAY DIFFRACTION99
2.4661-2.57830.2541530.2151708X-RAY DIFFRACTION99
2.5783-2.71410.29921550.21341701X-RAY DIFFRACTION99
2.7141-2.8840.20681400.20191716X-RAY DIFFRACTION99
2.884-3.10640.22721550.20021696X-RAY DIFFRACTION99
3.1064-3.41860.20751530.18961732X-RAY DIFFRACTION100
3.4186-3.91220.19221480.16431727X-RAY DIFFRACTION100
3.9122-4.9250.17441510.14111745X-RAY DIFFRACTION100
4.925-28.86160.22531540.17451772X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 6.9973 Å / Origin y: 0.037 Å / Origin z: 21.2772 Å
111213212223313233
T0.1973 Å2-0.008 Å20.0144 Å2-0.2234 Å2-0.0207 Å2--0.2242 Å2
L1.3354 °2-0.0849 °20.8603 °2-1.3769 °2-0.6291 °2--3.4619 °2
S0.0014 Å °-0.1507 Å °-0.0637 Å °0.1504 Å °0.0368 Å °-0.0269 Å °0.121 Å °-0.123 Å °-0.0213 Å °
Refinement TLS groupSelection details: all

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