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- PDB-7mev: Human Apex/Ref1 monomer with C138A mutation -

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Basic information

Entry
Database: PDB / ID: 7mev
TitleHuman Apex/Ref1 monomer with C138A mutation
ComponentsDNA-(apurinic or apyrimidinic site) endonuclease, mitochondrial
KeywordsDNA BINDING PROTEIN / Human Apex/Ref1 / DNase I / metal ion binding
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 / phosphodiesterase I activity / 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 / phosphodiesterase I activity / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / positive regulation of gene expression via chromosomal CpG island demethylation / Displacement of DNA glycosylase by APEX1 / phosphoric diester hydrolase activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / uracil DNA N-glycosylase activity / DNA catabolic process / 3'-5'-DNA exonuclease 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 / DNA-(apurinic or apyrimidinic site) endonuclease activity / regulation of mRNA stability / 3'-5' exonuclease activity / telomere maintenance / base-excision repair, gap-filling / cell redox homeostasis / DNA endonuclease activity / base-excision repair / chromatin DNA binding / transcription corepressor activity / RNA-DNA hybrid ribonuclease activity / regulation of apoptotic process / DNA recombination / endonuclease activity / chromosome, telomeric region / damaged DNA binding / 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 / nucleus / metal ion binding / 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. / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily
Similarity search - Domain/homology
DNA repair nuclease/redox regulator APEX1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNam, Y.W. / Yang, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)K08CA179084 United States
CitationJournal: To Be Published
Title: The Development of Novel Apurinic/Aprymidinic Endonuclease/Redox-factor 1 Inhibitors for the Treatment of Human Melanoma
Authors: Nam, Y.W. / Khanjani, E.B. / Fong, S. / Chawla, S. / Rahighi, S. / Ibrahim, N. / Parang, K. / Zhang, M. / Yang, S.
History
DepositionApr 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 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

Downloads & links

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Assembly

Deposited unit
A: DNA-(apurinic or apyrimidinic site) endonuclease, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4254
Polymers31,2171
Non-polymers2083
Water4,594255
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-9 kcal/mol
Surface area12070 Å2
Unit cell
Length a, b, c (Å)39.242, 74.447, 45.279
Angle α, β, γ (deg.)90.000, 111.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA-(apurinic or apyrimidinic site) endonuclease, mitochondrial / Apex/Ref1


Mass: 31216.590 Da / Num. of mol.: 1 / 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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
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: 1.97 Å3/Da / Density % sol: 37.56 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20 %w/v PEG 3350, 200 mM Sodium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Mar 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→21.377 Å / Num. obs: 31841 / % possible obs: 99.6 % / Redundancy: 1.9 % / Biso Wilson estimate: 12.02 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01464 / Rpim(I) all: 0.01464 / Rrim(I) all: 0.0207 / Net I/σ(I): 33.19
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.1593 / Mean I/σ(I) obs: 4.72 / Num. unique obs: 3081 / CC1/2: 0.935 / Rpim(I) all: 0.1593 / Rrim(I) all: 0.2252 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
XPREPdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7MCR

7mcr


Resolution: 1.6→21.377 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1959 1605 5.04 %
Rwork0.1674 30228 -
obs0.1689 31833 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.72 Å2 / Biso mean: 16.9546 Å2 / Biso min: 4.84 Å2
Refinement stepCycle: final / Resolution: 1.6→21.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 13 255 2460
Biso mean--17.41 24.71 -
Num. residues----275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062260
X-RAY DIFFRACTIONf_angle_d0.9083062
X-RAY DIFFRACTIONf_dihedral_angle_d3.4951356
X-RAY DIFFRACTIONf_chiral_restr0.055322
X-RAY DIFFRACTIONf_plane_restr0.006396
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.65160.25121310.1912269397
1.6516-1.71060.23421060.18892770100
1.7106-1.77910.22491810.18312698100
1.7791-1.860.23651520.17262739100
1.86-1.9580.20511470.17232767100
1.958-2.08060.2111410.16942734100
2.0806-2.24110.1961610.16742721100
2.2411-2.46630.22051490.17122755100
2.4663-2.82250.20221580.17222767100
2.8225-3.55340.20321450.15652766100
3.5534-3.60.13721340.13722818100

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