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- PDB-6mk3: Crystallographic solvent mapping analysis of DMSO bound to APE1 -

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Basic information

Entry
Database: PDB / ID: 6mk3
TitleCrystallographic solvent mapping analysis of DMSO bound to APE1
ComponentsDNA-(apurinic or apyrimidinic site) lyaseDNA-(apurinic or apyrimidinic site) lyase
KeywordsLYASE / Apurinic/apyrimidinic endonuclease / DNA repair / abasic site / solvent mapping
Function / homology
Function and homology information


Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity ...Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / phosphodiesterase I activity / Displacement of DNA glycosylase by APEX1 / 3'-5'-DNA exonuclease activity / phosphoric diester hydrolase activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / uracil DNA N-glycosylase activity / DNA demethylation / DNA catabolic process / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / PCNA-Dependent Long Patch Base Excision Repair / POLB-Dependent Long Patch Base Excision Repair / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / regulation of mRNA stability / telomere maintenance / cell redox homeostasis / DNA endonuclease activity / base-excision repair / chromatin DNA binding / transcription corepressor activity / RNA-DNA hybrid ribonuclease activity / endonuclease activity / regulation of apoptotic process / DNA recombination / damaged DNA binding / chromosome, telomeric region / transcription coactivator activity / oxidoreductase activity / ribosome / nuclear speck / DNA repair / centrosome / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
AP endonucleases family 1 signature 2. / AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase ...AP endonucleases family 1 signature 2. / AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / 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 repair nuclease/redox regulator APEX1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.478 Å
AuthorsGeorgiadis, M.M. / He, H. / Chen, Q.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA205166 United States
CitationJournal: J. Med. Chem. / Year: 2019
Title: Discovery of Macrocyclic Inhibitors of Apurinic/Apyrimidinic Endonuclease 1.
Authors: Trilles, R. / Beglov, D. / Chen, Q. / He, H. / Wireman, R. / Reed, A. / Chennamadhavuni, S. / Panek, J.S. / Brown, L.E. / Vajda, S. / Porco Jr., J.A. / Kelley, M.R. / Georgiadis, M.M.
History
DepositionSep 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,3546
Polymers32,0111
Non-polymers3425
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint16 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.583, 137.789, 45.243
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-748-

HOH

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Components

#1: Protein DNA-(apurinic or apyrimidinic site) lyase / DNA-(apurinic or apyrimidinic site) lyase / APEX nuclease / APEN / Apurinic-apyrimidinic endonuclease 1 / APE-1 / REF-1 / Redox factor-1


Mass: 32011.375 Da / Num. of mol.: 1 / Fragment: UNP residues 40-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APEX1, APE, APE1, APEX, APX, HAP1, REF1 / Production host: Escherichia coli (E. coli)
References: UniProt: P27695, Hydrolases; Acting on ester bonds, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES, pH 6.0, 200 mM sodium chloride, 18-21% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Aug 6, 2009
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.478→50 Å / Num. obs: 48453 / % possible obs: 97.6 % / Redundancy: 4.9 % / Biso Wilson estimate: 15.42 Å2 / Rmerge(I) obs: 0.06 / Χ2: 1.063 / Net I/σ(I): 14
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.48-1.513.60.4123651.002197.2
1.51-1.534.50.40624060.982199.5
1.53-1.564.90.30924651.0011100
1.56-1.595.20.28224421.063199.9
1.59-1.635.30.25624481.0221100
1.63-1.675.40.22124721.0221100
1.67-1.715.40.19524251.0721100
1.71-1.755.40.16324541.1131100
1.75-1.815.40.13624631.1011100
1.81-1.865.40.11124641.1641100
1.86-1.935.40.09624391.24199.8
1.93-2.015.30.0824631.208199.8
2.01-2.15.20.06824741.169199.9
2.1-2.215.10.05924771.123199.8
2.21-2.354.90.05224781.067199.8
2.35-2.534.80.04924260.943197.1
2.53-2.794.70.04723680.92194.9
2.79-3.194.50.03823360.953192.1
3.19-4.024.20.03821940.967185.4
4.02-503.50.0423940.912188

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX(phenix.refine)refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.478→37.818 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.41
RfactorNum. reflection% reflection
Rfree0.2186 2454 5.07 %
Rwork0.1908 --
obs0.1922 48386 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 67.074 Å2 / ksol: 0.408 e/Å3
Displacement parametersBiso max: 97.51 Å2 / Biso mean: 21.43 Å2 / Biso min: 5.82 Å2
Baniso -1Baniso -2Baniso -3
1--4.6102 Å20 Å20 Å2
2--4.3675 Å20 Å2
3---0.2426 Å2
Refinement stepCycle: final / Resolution: 1.478→37.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 20 252 2500
Biso mean--32.18 31.7 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052356
X-RAY DIFFRACTIONf_angle_d1.0293197
X-RAY DIFFRACTIONf_chiral_restr0.07336
X-RAY DIFFRACTIONf_plane_restr0.005419
X-RAY DIFFRACTIONf_dihedral_angle_d15.818872
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4784-1.50690.34811430.27292432257594
1.5069-1.53760.26961350.24725402675100
1.5376-1.57110.24751370.228325842721100
1.5711-1.60760.24351410.212625762717100
1.6076-1.64780.25491410.213625772718100
1.6478-1.69240.23181370.204825932730100
1.6924-1.74220.25521540.207525622716100
1.7422-1.79840.26661470.198825982745100
1.7984-1.86270.21961360.1926092745100
1.8627-1.93720.19081160.181826022718100
1.9372-2.02540.20461280.180826242752100
2.0254-2.13220.2021350.183225972732100
2.1322-2.26580.21961400.185426172757100
2.2658-2.44070.21931590.18412571273099
2.4407-2.68620.21791210.18142555267696
2.6862-3.07480.1991280.17322472260093
3.0748-3.87330.17081250.16122342246787
3.8733-37.82990.19831310.17472481261288

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