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- PDB-7n3y: Crystal Structure of Saccharomyces cerevisiae Apn2 Catalytic Doma... -

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Basic information

Entry
Database: PDB / ID: 7n3y
TitleCrystal Structure of Saccharomyces cerevisiae Apn2 Catalytic Domain E59Q/D222N Mutant in Complex with DNA
Components
  • DNA (5'-D(*CP*CP*GP*AP*AP*AP*TP*TP*(PST)P*(SC)P*(GS)P*(GS)P*(AS))-3')
  • DNA (5'-D(*TP*CP*CP*GP*AP*AP*AP*TP*(PST)P*(PST)P*(SC)P*(GS)P*(GS))-3')
  • DNA-(apurinic or apyrimidinic site) endonuclease 2
KeywordsHYDROLASE/DNA / nuclease / DNA complex / EEP fold / APE2 homolog / HYDROLASE / HYDROLASE-DNA complex
Function / homology
Function and homology information


double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / phosphoric diester hydrolase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / base-excision repair / endonuclease activity / DNA binding / zinc ion binding / nucleus
Similarity search - Function
Zinc finger GRF-type profile. / Zinc finger, GRF-type / GRF zinc finger / AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / AP endonuclease 1 / AP endonucleases family 1 profile. / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily
Similarity search - Domain/homology
CITRIC ACID / D(-)-TARTARIC ACID / L(+)-TARTARIC ACID / DNA / DNA (> 10) / DNA-(apurinic or apyrimidinic site) endonuclease 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsWojtaszek, J.L. / Krahn, J. / 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
B: DNA-(apurinic or apyrimidinic site) endonuclease 2
C: DNA-(apurinic or apyrimidinic site) endonuclease 2
D: DNA-(apurinic or apyrimidinic site) endonuclease 2
E: DNA (5'-D(*TP*CP*CP*GP*AP*AP*AP*TP*(PST)P*(PST)P*(SC)P*(GS)P*(GS))-3')
F: DNA (5'-D(*TP*CP*CP*GP*AP*AP*AP*TP*(PST)P*(PST)P*(SC)P*(GS)P*(GS))-3')
G: DNA (5'-D(*TP*CP*CP*GP*AP*AP*AP*TP*(PST)P*(PST)P*(SC)P*(GS)P*(GS))-3')
H: DNA (5'-D(*CP*CP*GP*AP*AP*AP*TP*TP*(PST)P*(SC)P*(GS)P*(GS)P*(AS))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,38015
Polymers205,4858
Non-polymers8957
Water1,802100
1
A: DNA-(apurinic or apyrimidinic site) endonuclease 2
B: DNA-(apurinic or apyrimidinic site) endonuclease 2
E: DNA (5'-D(*TP*CP*CP*GP*AP*AP*AP*TP*(PST)P*(PST)P*(SC)P*(GS)P*(GS))-3')
F: DNA (5'-D(*TP*CP*CP*GP*AP*AP*AP*TP*(PST)P*(PST)P*(SC)P*(GS)P*(GS))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3329
Polymers102,7384
Non-polymers5945
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA-(apurinic or apyrimidinic site) endonuclease 2
D: DNA-(apurinic or apyrimidinic site) endonuclease 2
G: DNA (5'-D(*TP*CP*CP*GP*AP*AP*AP*TP*(PST)P*(PST)P*(SC)P*(GS)P*(GS))-3')
H: DNA (5'-D(*CP*CP*GP*AP*AP*AP*TP*TP*(PST)P*(SC)P*(GS)P*(GS)P*(AS))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0476
Polymers102,7474
Non-polymers3002
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.408, 101.473, 144.973
Angle α, β, γ (deg.)90.00, 90.14, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 47322.094 Da / Num. of mol.: 4 / Mutation: E59Q,D222N
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

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DNA chain , 2 types, 4 molecules EFGH

#2: DNA chain DNA (5'-D(*TP*CP*CP*GP*AP*AP*AP*TP*(PST)P*(PST)P*(SC)P*(GS)P*(GS))-3')


Mass: 4046.927 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*CP*GP*AP*AP*AP*TP*TP*(PST)P*(SC)P*(GS)P*(GS)P*(AS))-3')


Mass: 4055.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 107 molecules

#4: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#7: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium citrate, 20% PEG 3350

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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 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.73→36.97 Å / Num. obs: 51375 / % possible obs: 96.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 67.86 Å2 / Rrim(I) all: 0.085 / Net I/σ(I): 18.4
Reflection shellResolution: 2.73→2.83 Å / Mean I/σ(I) obs: 1.44 / Num. unique obs: 4598 / Rrim(I) all: 0.891

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G0R

3g0r


Resolution: 2.73→36.97 Å / SU ML: 0.333 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.917
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.228 1894 3.69 %
Rwork0.2 --
obs0.201 51347 95.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 101.5 Å2
Refinement stepCycle: LAST / Resolution: 2.73→36.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11597 1036 58 100 12791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413055
X-RAY DIFFRACTIONf_angle_d0.6117862
X-RAY DIFFRACTIONf_dihedral_angle_d12.9044734
X-RAY DIFFRACTIONf_chiral_restr0.0472014
X-RAY DIFFRACTIONf_plane_restr0.0042140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.80.31791120.28032989X-RAY DIFFRACTION81
2.8-2.870.28541380.26353607X-RAY DIFFRACTION98
2.87-2.960.32351390.25773584X-RAY DIFFRACTION98
2.96-3.050.2791410.24553574X-RAY DIFFRACTION98
3.05-3.160.26841430.25323640X-RAY DIFFRACTION98
3.16-3.290.27121360.21983569X-RAY DIFFRACTION97
3.29-3.440.21891320.21093572X-RAY DIFFRACTION97
3.44-3.620.22531420.20253597X-RAY DIFFRACTION97
3.62-3.840.2571310.19773599X-RAY DIFFRACTION97
3.84-4.140.22651380.18563560X-RAY DIFFRACTION97
4.14-4.560.22221320.17583564X-RAY DIFFRACTION96
4.56-5.210.19651390.1763555X-RAY DIFFRACTION96
5.21-6.560.22491350.20263544X-RAY DIFFRACTION95
6.56-36.970.19471360.18263499X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: 5.1379 Å / Origin y: 20.3876 Å / Origin z: 32.6817 Å
111213212223313233
T0.5193 Å20.0399 Å2-0.0076 Å2-0.6846 Å2-0.0636 Å2--0.6381 Å2
L0.5839 °20.0274 °2-0.1047 °2-0.2225 °20.0158 °2--0.3844 °2
S0.0023 Å °-0.5048 Å °0.0482 Å °0.0926 Å °0.012 Å °-0.0062 Å °-0.0181 Å °0.199 Å °-0.0072 Å °
Refinement TLS groupSelection details: ALL

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