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

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Basic information

Entry
Database: PDB / ID: 6bos
TitleHuman APE1 substrate complex with an A/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 DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / Displacement of DNA glycosylase by APEX1 ...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 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 / double-stranded telomeric DNA binding / 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 / 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 / RNA-DNA hybrid ribonuclease activity / transcription corepressor activity / endonuclease activity / DNA recombination / regulation of apoptotic process / damaged DNA binding / transcription coactivator activity / oxidoreductase activity / chromosome, telomeric region / 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: 2.304 Å
AuthorsFreudenthal, B.D. / Whitaker, A.M. / Fairlamb, M.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES024431 United States
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 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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


Theoretical massNumber of molelcules
Total (without water)83,9784
Polymers83,9784
Non-polymers00
Water3,603200
1
A: DNA-(apurinic or apyrimidinic site) lyase
P: 21-mer DNA
V: 21-mer DNA


Theoretical massNumber of molelcules
Total (without water)48,3723
Polymers48,3723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA-(apurinic or apyrimidinic site) lyase


Theoretical massNumber of molelcules
Total (without water)35,6061
Polymers35,6061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.275, 60.734, 72.475
Angle α, β, γ (deg.)83.660, 79.240, 88.360
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: 35606.492 Da / Num. of mol.: 2
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: 6433.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 45.8 % / Mosaicity: 1.093 °
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: Feb 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 58993 / % possible obs: 99.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 34.86 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.048 / Rrim(I) all: 0.102 / Χ2: 1.548 / Net I/σ(I): 12.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.31-2.352.30.50916300.7810.3940.6460.98999.3
2.35-2.392.40.48515620.8030.3720.6141.03698.7
2.39-2.442.50.45516340.8320.3470.5751.04299.6
2.44-2.492.50.40716090.8690.3070.5121.01599.6
2.49-2.542.60.35815880.850.2610.4451.74299.2
2.54-2.62.80.32416390.9080.2330.4011.13899.8
2.6-2.672.90.29715980.9180.2060.3631.21999.8
2.67-2.743.10.25316250.9390.170.3061.20999.7
2.74-2.823.20.2215880.9580.1440.2641.385100
2.82-2.913.40.19516440.9660.1220.2321.64399.9
2.91-3.013.60.17816320.9760.1080.2091.47599.9
3.01-3.133.90.14616030.9810.0850.1691.34100
3.13-3.284.20.12816180.9830.0720.1482.185100
3.28-3.454.50.10416210.9850.0550.1181.84999.9
3.45-3.664.90.12416250.5620.0670.1412.22599.9
3.66-3.955.70.08116090.9930.0380.0891.958100
3.95-4.345.80.06516330.9960.030.0711.512100
4.34-4.975.70.05616230.9970.0260.0621.415100
4.97-6.245.50.05516050.9970.0260.0611.447100
6.24-255.30.04916200.9970.0230.0541.387100

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Processing

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

5dff


Resolution: 2.304→24.892 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.14
RfactorNum. reflection% reflection
Rfree0.2358 3636 6.16 %
Rwork0.1927 --
obs0.1955 58993 90.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.38 Å2 / Biso mean: 37.3302 Å2 / Biso min: 14.4 Å2
Refinement stepCycle: final / Resolution: 2.304→24.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4269 845 0 200 5314
Biso mean---35.72 -
Num. residues----583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055463
X-RAY DIFFRACTIONf_angle_d0.8317576
X-RAY DIFFRACTIONf_chiral_restr0.045811
X-RAY DIFFRACTIONf_plane_restr0.005824
X-RAY DIFFRACTIONf_dihedral_angle_d20.8773132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3043-2.33460.29721140.26751680179471
2.3346-2.36660.3061240.28081881200583
2.3666-2.40040.33091150.28761951206682
2.4004-2.43620.341290.26891985211483
2.4362-2.47420.31941240.27131996212085
2.4742-2.51470.32321330.271962209586
2.5147-2.55810.3081390.2582082222186
2.5581-2.60450.38051290.25652004213386
2.6045-2.65460.31021330.25832055218889
2.6546-2.70870.31191380.24772069220789
2.7087-2.76750.30591420.23462171231389
2.7675-2.83180.28931360.23412006214290
2.8318-2.90250.2451430.2352150229391
2.9025-2.98090.30621450.25512197234292
2.9809-3.06840.29171390.25082173231293
3.0684-3.16730.28581510.23242267241894
3.1673-3.28030.25811450.1962191233694
3.2803-3.41130.21971490.18492251240095
3.4113-3.56610.22541500.17582193234395
3.5661-3.75350.22921510.1712279243098
3.7535-3.98780.21721530.16232332248598
3.9878-4.29430.18211520.14722296244898
4.2943-4.72370.18281510.14422310246199
4.7237-5.40120.16021490.15032312246198
5.4012-6.78210.18981560.16232301245798
6.7821-24.89380.20061460.15912263240996

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