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- PDB-6bot: Human APE1 substrate complex with an C/C mismatch adjacent the THF -

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Basic information

Entry
Database: PDB / ID: 6bot
TitleHuman APE1 substrate complex with an C/C mismatch adjacent the THF
Components
  • (21-mer DNA) x 2
  • DNA-(apurinic or apyrimidinic site) lyase
KeywordsDNA BINDING PROTEIN/DNA / HYDROLASE LYASE / DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Resolution of Abasic Sites (AP sites) / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / : / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III ...Resolution of Abasic Sites (AP sites) / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / : / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / Displacement of DNA glycosylase by APEX1 / 3'-5'-DNA exonuclease activity / positive regulation of gene expression via chromosomal CpG island demethylation / phosphoric diester hydrolase activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / uracil DNA N-glycosylase activity / DNA catabolic process / phosphodiesterase I activity / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / base-excision repair, gap-filling / regulation of mRNA stability / 3'-5' exonuclease activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / telomere maintenance / cell redox homeostasis / DNA endonuclease activity / base-excision repair / chromatin DNA binding / RNA-DNA hybrid ribonuclease activity / transcription corepressor activity / endonuclease activity / regulation of apoptotic process / DNA recombination / damaged DNA binding / transcription coactivator activity / chromosome, telomeric region / oxidoreductase activity / nuclear speck / ribosome / 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 / DNA (> 10) / DNA repair nuclease/redox regulator APEX1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFreudenthal, B.D. / Whitaker, A.M. / Fairlamb, M.S.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches.
Authors: Fairlamb, M.S. / Whitaker, A.M. / Freudenthal, B.D.
History
DepositionNov 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: DNA-(apurinic or apyrimidinic site) lyase
P: 21-mer DNA
V: 21-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,9525
Polymers83,8904
Non-polymers621
Water4,053225
1
A: DNA-(apurinic or apyrimidinic site) lyase
P: 21-mer DNA
V: 21-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3784
Polymers48,3163
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-19 kcal/mol
Surface area17750 Å2
MethodPISA
2
B: DNA-(apurinic or apyrimidinic site) lyase


Theoretical massNumber of molelcules
Total (without water)35,5741
Polymers35,5741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.247, 60.944, 73.292
Angle α, β, γ (deg.)83.18, 78.48, 87.21
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 35574.426 Da / Num. of mol.: 2 / Mutation: C138A
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: DNA chain 21-mer DNA


Mass: 6332.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain 21-mer DNA


Mass: 6409.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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.: 225 / 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: 2.29 Å3/Da / Density % sol: 46.32 % / Mosaicity: 1.708 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 62321 / % possible obs: 99.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 39.18 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.9
Reflection shellResolution: 2.32→2.36 Å / Redundancy: 3 % / Rmerge(I) obs: 0.573 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DFF

5dff


Resolution: 2.3→48.91 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 3789 6.08 %
Rwork0.202 --
obs0.204 62321 94.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4226 843 4 225 5298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055397
X-RAY DIFFRACTIONf_angle_d0.9887486
X-RAY DIFFRACTIONf_dihedral_angle_d19.5663075
X-RAY DIFFRACTIONf_chiral_restr0.045808
X-RAY DIFFRACTIONf_plane_restr0.005814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.32920.371990.29161629X-RAY DIFFRACTION70
2.3292-2.35990.32091310.30351972X-RAY DIFFRACTION88
2.3599-2.39220.37341350.28072081X-RAY DIFFRACTION90
2.3922-2.42640.33071380.26742132X-RAY DIFFRACTION91
2.4264-2.46260.2841410.26712117X-RAY DIFFRACTION93
2.4626-2.50110.30511390.28232134X-RAY DIFFRACTION92
2.5011-2.54210.41311450.26312179X-RAY DIFFRACTION95
2.5421-2.58590.33691410.26732171X-RAY DIFFRACTION95
2.5859-2.63290.35371520.25492254X-RAY DIFFRACTION96
2.6329-2.68360.23621380.23972086X-RAY DIFFRACTION95
2.6836-2.73830.31251450.2532225X-RAY DIFFRACTION96
2.7383-2.79790.26581460.24272246X-RAY DIFFRACTION96
2.7979-2.8630.33191430.25092170X-RAY DIFFRACTION96
2.863-2.93450.34581440.26082259X-RAY DIFFRACTION96
2.9345-3.01390.38291360.28672139X-RAY DIFFRACTION95
3.0139-3.10260.28951470.27142252X-RAY DIFFRACTION96
3.1026-3.20270.26691410.2212273X-RAY DIFFRACTION96
3.2027-3.31710.27491380.20122194X-RAY DIFFRACTION97
3.3171-3.44990.21711450.19722226X-RAY DIFFRACTION97
3.4499-3.60690.2221410.1872220X-RAY DIFFRACTION97
3.6069-3.7970.25531380.18142224X-RAY DIFFRACTION97
3.797-4.03470.20551520.17662295X-RAY DIFFRACTION97
4.0347-4.34610.18071440.15582197X-RAY DIFFRACTION97
4.3461-4.78310.19231440.14682214X-RAY DIFFRACTION98
4.7831-5.47440.181460.1532244X-RAY DIFFRACTION97
5.4744-6.89420.16481420.17232240X-RAY DIFFRACTION97
6.8942-48.92210.21821380.16282159X-RAY DIFFRACTION94

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