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- PDB-8ka3: Arabidopsis AP endonuclease ARP complex with 22bp THF-containing DNA -

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Basic information

Entry
Database: PDB / ID: 8ka3
TitleArabidopsis AP endonuclease ARP complex with 22bp THF-containing DNA
Components
  • DNA (43-MER)
  • DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic
KeywordsHYDROLASE/DNA / AP / abasic site / endonuclease / Arabidopsis / HYDROLASE-DNA complex
Function / homology
Function and homology information


chloroplast nucleoid / phosphodiesterase I activity / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / phosphatase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / base-excision repair / endonuclease activity / positive regulation of DNA-templated transcription ...chloroplast nucleoid / phosphodiesterase I activity / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / phosphatase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / base-excision repair / endonuclease activity / positive regulation of DNA-templated transcription / DNA binding / nucleus / metal ion binding
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. / SAP domain superfamily / AP endonuclease 1 / AP endonucleases family 1 profile. / SAP domain / SAP motif profile. ...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. / SAP domain superfamily / AP endonuclease 1 / AP endonucleases family 1 profile. / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily
Similarity search - Domain/homology
1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE / NICKEL (II) ION / DNA / DNA (> 10) / DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGuo, W.T. / Wu, B.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Structural insights into the catalytic mechanism of the AP endonuclease AtARP.
Authors: Guo, W. / Wu, W. / Wen, Y. / Gao, Y. / Zhuang, S. / Meng, C. / Chen, H. / Zhao, Z. / Hu, K. / Wu, B.
History
DepositionAug 2, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct.title
Revision 1.2Apr 3, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 19, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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, chloroplastic
D: DNA (43-MER)
C: DNA (43-MER)
F: DNA (43-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7546
Polymers73,4984
Non-polymers2572
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-33 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.731, 52.295, 71.095
Angle α, β, γ (deg.)90.000, 117.030, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic / Apurinic endonuclease-redox protein


Mass: 33704.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ARP, REF, At2g41460, T26J13.5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P45951, exodeoxyribonuclease III
#2: DNA chain DNA (43-MER)


Mass: 13264.459 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-3DR / 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE / ABASIC DIDEOXYRIBOSE


Type: DNA linking / Mass: 198.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O6P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.54 Å3/Da / Density % sol: 20.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% (w/v) PEG 1500, 0.1M PCB/Sodium hydroxide pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 8713 / % possible obs: 94.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 74.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.058 / Rrim(I) all: 0.149 / Net I/σ(I): 10.3
Reflection shellResolution: 3→3.16 Å / Rmerge(I) obs: 1.182 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1348 / CC1/2: 0.678 / Rpim(I) all: 0.494 / Rrim(I) all: 1.283

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→29.7 Å / SU ML: 0.3739 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.6193
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.302 439 5.05 %
Rwork0.2419 8248 -
obs0.2447 8687 94.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.72 Å2
Refinement stepCycle: LAST / Resolution: 3→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3144 0 1 3 3148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00283308
X-RAY DIFFRACTIONf_angle_d0.53294681
X-RAY DIFFRACTIONf_chiral_restr0.0377519
X-RAY DIFFRACTIONf_plane_restr0.0033449
X-RAY DIFFRACTIONf_dihedral_angle_d30.1745743
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.420.33691640.33912812X-RAY DIFFRACTION99.77
3.45-4.320.32081570.26682485X-RAY DIFFRACTION88.48
4.32-29.70.27071180.20282951X-RAY DIFFRACTION99.45
Refinement TLS params.Method: refined / Origin x: -34.5353661276 Å / Origin y: 12.7758116059 Å / Origin z: 20.7378100033 Å
111213212223313233
T0.863174230962 Å2-0.0312447386229 Å2-0.189181104969 Å2-0.483058764754 Å20.000240283019942 Å2--0.54803303957 Å2
L2.53360269601 °20.250796286863 °2-0.642196734524 °2-1.696853607 °2-0.430792558894 °2--3.64374919329 °2
S0.0809591709109 Å °-0.40112995569 Å °-0.217370599315 Å °0.254232675613 Å °-0.137882391286 Å °0.262700790607 Å °0.0335807192509 Å °-0.144706020147 Å °0.0488841217402 Å °
Refinement TLS groupSelection details: all

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