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- PDB-7n3z: Crystal Structure of Saccharomyces cerevisiae Apn2 Catalytic Domain -

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Basic information

Entry
Database: PDB / ID: 7n3z
TitleCrystal Structure of Saccharomyces cerevisiae Apn2 Catalytic Domain
ComponentsDNA-(apurinic or apyrimidinic site) endonuclease 2
KeywordsHYDROLASE / nuclease / DNA repair / EEP fold / APE2 homolog
Function / homology
Function and homology information


double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / phosphoric diester hydrolase activity / 3'-5' exonuclease activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / endonuclease activity / DNA binding / zinc ion binding / nucleus
Similarity search - Function
Zinc finger, GRF-type / GRF zinc finger / Zinc finger GRF-type profile. / AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase ...Zinc finger, GRF-type / GRF zinc finger / Zinc finger GRF-type profile. / AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA-(apurinic or apyrimidinic site) endonuclease 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsWojtaszek, J.L. / Wallace, B.D. / Williams, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1Z01ES102765 United States
CitationJournal: Cell Rep / Year: 2022
Title: Molecular basis for processing of topoisomerase 1-triggered DNA damage by Apn2/APE2.
Authors: Williams, J.S. / Wojtaszek, J.L. / Appel, D.C. / Krahn, J. / Wallace, B.D. / Walsh, E. / Kunkel, T.A. / Williams, R.S.
History
DepositionJun 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-(apurinic or apyrimidinic site) endonuclease 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4464
Polymers47,3241
Non-polymers1223
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.412, 46.948, 51.532
Angle α, β, γ (deg.)90.000, 104.213, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-815-

HOH

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Components

#1: Protein DNA-(apurinic or apyrimidinic site) endonuclease 2 / AP endonuclease 2 / Apurinic-apyrimidinic endonuclease 2


Mass: 47324.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: APN2, ETH1, YBL019W, YBL0443 / Production host: Escherichia coli (E. coli)
References: UniProt: P38207, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 25% PEG 6000

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→36.67 Å / Num. obs: 26508 / % possible obs: 97.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.33 Å2 / Rrim(I) all: 0.107 / Net I/σ(I): 14.42
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.99 / Num. unique obs: 2254 / Rrim(I) all: 0.548 / % possible all: 83.2

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3g0r

3g0r


Resolution: 1.99→36.67 Å / SU ML: 0.1871 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.3319
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1978 1264 4.77 %
Rwork0.1627 25231 -
obs0.1644 26495 96.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.52 Å2
Refinement stepCycle: LAST / Resolution: 1.99→36.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2997 0 6 226 3229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083079
X-RAY DIFFRACTIONf_angle_d0.91544171
X-RAY DIFFRACTIONf_chiral_restr0.0537471
X-RAY DIFFRACTIONf_plane_restr0.0054540
X-RAY DIFFRACTIONf_dihedral_angle_d14.19941158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.070.25511150.2122180X-RAY DIFFRACTION76.55
2.07-2.170.22271310.19512725X-RAY DIFFRACTION94.13
2.17-2.280.20861220.17112868X-RAY DIFFRACTION99.83
2.28-2.430.1971500.16642890X-RAY DIFFRACTION99.97
2.43-2.610.22171640.17322887X-RAY DIFFRACTION99.9
2.61-2.880.20411350.16572885X-RAY DIFFRACTION99.87
2.88-3.290.19641630.16572876X-RAY DIFFRACTION99.84
3.29-4.150.20261390.14852923X-RAY DIFFRACTION99.9
4.15-36.670.16881450.15412997X-RAY DIFFRACTION99.75

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