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

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Basic information

Entry
Database: PDB / ID: 6bov
TitleHuman APE1 substrate complex with an A/G mismatch adjacent the THF
Components
  • (21-mer DNA) x 2
  • DNA-(apurinic or apyrimidinic site) lyaseDNA-(apurinic or apyrimidinic site) lyase
KeywordsDNA BINDING PROTEIN/DNA / HYDROLASE LYASE / DNA / DNA BINDING PROTEIN-DNA complex
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
DI(HYDROXYETHYL)ETHER / 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: 1.975 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0405
Polymers83,9344
Non-polymers1061
Water5,062281
1
A: DNA-(apurinic or apyrimidinic site) lyase
P: 21-mer DNA
V: 21-mer DNA


Theoretical massNumber of molelcules
Total (without water)48,3623
Polymers48,3623
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-15 kcal/mol
Surface area17510 Å2
MethodPISA
2
B: DNA-(apurinic or apyrimidinic site) lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6792
Polymers35,5721
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.358, 60.371, 73.343
Angle α, β, γ (deg.)83.56, 78.43, 88.30
Int Tables number1
Space group name H-MP1

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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: 35572.457 Da / Num. of mol.: 2 / Mutation: E96Q, D210N, 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: 6356.074 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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.28 Å3/Da / Density % sol: 46 % / Mosaicity: 0.957 °
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: Apr 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.975→25 Å / Num. obs: 98881 / % possible obs: 100 % / Redundancy: 4.3 % / Biso Wilson estimate: 31.04 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.033 / Rrim(I) all: 0.078 / Χ2: 1.499 / Net I/σ(I): 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-2.012.50.47326520.8010.3590.5970.99199.8
2.01-2.052.60.36125330.8280.2690.4521.00899.7
2.05-2.092.70.29725710.740.2220.3731.31999.9
2.09-2.132.70.26726160.8970.1950.3321.061100
2.13-2.182.80.23825630.9270.1710.2941.123100
2.18-2.232.90.23926600.930.1660.2921.36100
2.23-2.293.10.23725280.9140.1580.2861.584100
2.29-2.353.30.20626160.9630.1310.2451.297100
2.35-2.423.60.18525910.9670.1130.2181.255100
2.42-2.493.80.16425770.9720.0960.191.499100
2.49-2.5840.1525920.9790.0850.1731.534100
2.58-2.694.40.13925740.9830.0740.1581.547100
2.69-2.814.80.12526020.9850.0630.141.643100
2.81-2.965.30.11126150.990.0540.1241.385100
2.96-3.1460.10125780.9930.0450.1112.413100
3.14-3.386.60.08625840.9950.0360.0932.21100
3.38-3.726.50.07526150.9960.0320.0811.445100
3.72-4.266.50.05925670.9970.0250.0641.417100
4.26-5.366.40.04825910.9980.0210.0521.132100
5.36-256.20.04725940.9980.020.0511.188100

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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: 1.975→24.771 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2423 3825 3.87 %
Rwork0.2109 --
obs0.2122 98881 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.975→24.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4224 848 5 281 5358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115381
X-RAY DIFFRACTIONf_angle_d1.1767468
X-RAY DIFFRACTIONf_dihedral_angle_d19.1833063
X-RAY DIFFRACTIONf_chiral_restr0.059806
X-RAY DIFFRACTIONf_plane_restr0.007811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9745-1.99950.38051310.31573112X-RAY DIFFRACTION82
1.9995-2.02580.28661320.3033331X-RAY DIFFRACTION91
2.0258-2.05360.33431380.28033440X-RAY DIFFRACTION92
2.0536-2.08290.28921350.2743409X-RAY DIFFRACTION92
2.0829-2.1140.29431400.27763461X-RAY DIFFRACTION92
2.114-2.1470.29851330.26513353X-RAY DIFFRACTION93
2.147-2.18210.30921330.26563470X-RAY DIFFRACTION93
2.1821-2.21980.32091440.26713554X-RAY DIFFRACTION94
2.2198-2.26010.30481340.26083334X-RAY DIFFRACTION94
2.2601-2.30350.28581460.26363572X-RAY DIFFRACTION94
2.3035-2.35050.32181410.27413492X-RAY DIFFRACTION94
2.3505-2.40160.34881400.27183455X-RAY DIFFRACTION95
2.4016-2.45740.35431420.25353604X-RAY DIFFRACTION95
2.4574-2.51880.2661420.25293527X-RAY DIFFRACTION96
2.5188-2.58680.28531430.25343516X-RAY DIFFRACTION96
2.5868-2.66290.30821440.25113508X-RAY DIFFRACTION96
2.6629-2.74870.3411450.25163603X-RAY DIFFRACTION96
2.7487-2.84680.28591440.23633591X-RAY DIFFRACTION96
2.8468-2.96060.28791440.24533567X-RAY DIFFRACTION97
2.9606-3.09510.21721450.22813594X-RAY DIFFRACTION97
3.0951-3.2580.30751440.21853593X-RAY DIFFRACTION98
3.258-3.46160.26021480.19573695X-RAY DIFFRACTION98
3.4616-3.7280.21771470.18623682X-RAY DIFFRACTION99
3.728-4.10170.21021470.1793647X-RAY DIFFRACTION99
4.1017-4.69170.15631460.15423651X-RAY DIFFRACTION99
4.6917-5.89780.16591480.16253660X-RAY DIFFRACTION99
5.8978-24.7730.19131490.16713635X-RAY DIFFRACTION98

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