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- PDB-1y97: The human TREX2 3' exonuclease structure suggests a mechanism for... -

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Basic information

Entry
Database: PDB / ID: 1y97
TitleThe human TREX2 3' exonuclease structure suggests a mechanism for efficient non-processive DNA catalysis
ComponentsThree prime repair exonuclease 2
KeywordsHYDROLASE / TREX2 / exonuclease
Function / homology
Function and homology information


: / : / exodeoxyribonuclease III / 3'-5'-DNA exonuclease activity / DNA metabolic process / nucleic acid binding / DNA repair / magnesium ion binding / protein homodimerization activity / nucleus / cytoplasm
Similarity search - Function
Three prime repair exonuclease 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsPerrino, F.W. / Harvey, S. / McMillin, S. / Hollis, T.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The Human TREX2 3' -> 5'-Exonuclease Structure Suggests a Mechanism for Efficient Nonprocessive DNA Catalysis.
Authors: Perrino, F.W. / Harvey, S. / McMillin, S. / Hollis, T.
History
DepositionDec 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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


Theoretical massNumber of molelcules
Total (without water)52,4492
Polymers52,4492
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-8 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.5, 77.2, 101.7
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Detailsbiological assembly is dimer in asymmetric unit

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Components

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


Mass: 26224.346 Da / Num. of mol.: 2 / Fragment: TREX2 exonuclease
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TREX2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BQ50, exodeoxyribonuclease III
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 1.99 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.4 M ammonium phosphate, 7% PEG400, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97832, 0.97876, 0.9500
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Mar 30, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978321
20.978761
30.951
ReflectionResolution: 2.47→30 Å / Num. all: 14781 / Num. obs: 14344 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 5 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 19
Reflection shellResolution: 2.47→2.55 Å / Redundancy: 2 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4 / Num. unique all: 1432 / Rsym value: 0.18 / % possible all: 80

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.5→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1405 -random
Rwork0.205 ---
all0.205 14781 --
obs0.205 14344 97 %-
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3263 0 0 77 3340
LS refinement shellResolution: 2.5→2.61 Å
RfactorNum. reflection
Rfree0.301 91
Rwork0.223 -
obs-1442

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