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- PDB-7mcr: Human Apex/Ref1 homodimer formed under oxidative condition -

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Basic information

Entry
Database: PDB / ID: 7mcr
TitleHuman Apex/Ref1 homodimer formed under oxidative condition
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: 1.9 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. / Parang, K. / Zhang, M. / Yang, S.
History
DepositionApr 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 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)31,2732
Polymers31,2491
Non-polymers241
Water5,585310
1
A: DNA-(apurinic or apyrimidinic site) endonuclease, mitochondrial
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)62,5464
Polymers62,4972
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)77.042, 44.794, 77.436
Angle α, β, γ (deg.)90.000, 92.270, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-694-

HOH

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Components

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


Mass: 31248.656 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM MES/ sodium hydroxide, 200 mM calcium acetate, 20% W/V PEG 8000

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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: Jul 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→27.843 Å / Num. obs: 21090 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 13.43 Å2 / CC1/2: 0.943 / Rpim(I) all: 0.132 / Rrim(I) all: 0.248 / Net I/σ(I): 21.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2010 / CC1/2: 0.69 / Rpim(I) all: 0.503 / Rrim(I) all: 0.844 / % possible all: 94.9

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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: 5cfg

5cfg


Resolution: 1.9→27.843 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2326 1805 9.43 %
Rwork0.1634 17340 -
obs0.1699 19145 90.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.52 Å2 / Biso mean: 20.5952 Å2 / Biso min: 4.66 Å2
Refinement stepCycle: final / Resolution: 1.9→27.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 0 310 2503
Biso mean---27.72 -
Num. residues----275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062251
X-RAY DIFFRACTIONf_angle_d0.8713053
X-RAY DIFFRACTIONf_dihedral_angle_d3.1421353
X-RAY DIFFRACTIONf_chiral_restr0.049322
X-RAY DIFFRACTIONf_plane_restr0.005396
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9001-1.95150.32351160.2385108674
1.9515-2.00890.25511110.206113578
2.0089-2.07370.26191030.1792120683
2.0737-2.14780.2451530.1719125386
2.1478-2.23380.28041280.1724131590
2.2338-2.33540.25611450.1737131592
2.3354-2.45840.28351440.1733137994
2.4584-2.61240.27781390.1756137494
2.6124-2.81390.24591470.1768143297
2.8139-3.09670.24851560.167143499
3.0967-3.54410.20271450.144145899
3.5441-4.46220.18881510.1304148299
4.4622-4.80.1821670.1541147198
Refinement TLS params.Method: refined / Origin x: 7.8199 Å / Origin y: -0.6453 Å / Origin z: 18.598 Å
111213212223313233
T0.0349 Å20.0167 Å20.0045 Å2-0.0442 Å2-0.0031 Å2--0.0446 Å2
L0.647 °20.0321 °20.3292 °2-1.2003 °20.0966 °2--1.3443 °2
S0.0278 Å °-0.0123 Å °0.0002 Å °0.0649 Å °-0.018 Å °-0.0081 Å °0.0425 Å °-0.0213 Å °0.0013 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA44 - 318
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allS1 - 310

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