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- PDB-8ka4: Arabidopsis AP endonuclease ARP complex with 21bp THF-containing DNA -

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Basic information

Entry
Database: PDB / ID: 8ka4
TitleArabidopsis AP endonuclease ARP complex with 21bp THF-containing DNA
ComponentsDNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic
KeywordsHYDROLASE / AP / abasic site / endonuclease / Arabidopsis
Function / homology
Function and homology information


chloroplast nucleoid / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / phosphoric diester hydrolase activity / phosphodiesterase I activity / phosphatase activity / 3'-5' exonuclease activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / nucleotide-excision repair / base-excision repair ...chloroplast nucleoid / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / phosphoric diester hydrolase activity / phosphodiesterase I activity / phosphatase activity / 3'-5' exonuclease activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / nucleotide-excision repair / base-excision repair / DNA repair / positive regulation of DNA-templated transcription / DNA binding / metal ion binding / nucleus
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. / SAP domain superfamily / SAP motif profile. / SAP domain ...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. / SAP domain superfamily / SAP motif profile. / SAP domain / 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
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / PHOSPHATE ION / DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 2.0May 29, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.value_order / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id
Revision 2.1Jun 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
B: DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic
C: DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic
D: DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,89110
Polymers134,8174
Non-polymers1,0746
Water7,440413
1
A: DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic


Theoretical massNumber of molelcules
Total (without water)33,7041
Polymers33,7041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2414
Polymers33,7041
Non-polymers5373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1463
Polymers33,7041
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7992
Polymers33,7041
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.154, 102.215, 169.198
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 241 through 254 or (resid 255...
d_2ens_1(chain "B" and (resid 241 through 250 or (resid 251...
d_3ens_1(chain "C" and (resid 241 through 254 or (resid 255...
d_4ens_1(chain "D" and (resid 241 through 250 or (resid 251...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERTHRTHRAA241 - 3642 - 125
d_12THRTHRPHEPHEAA371 - 380132 - 141
d_13SERSERLEULEUAA382 - 536143 - 297
d_21SERSERTHRTHRBB241 - 3642 - 125
d_22THRTHRPHEPHEBB371 - 380132 - 141
d_23SERSERLEULEUBB382 - 536143 - 297
d_31SERSERTHRTHRCC241 - 3642 - 125
d_32THRTHRPHEPHECC371 - 380132 - 141
d_33SERSERLEULEUCC382 - 536143 - 297
d_41SERSERPHEPHEDD241 - 3802 - 141
d_42SERSERLEULEUDD382 - 536143 - 297

NCS oper:
IDCodeMatrixVector
1given(0.169547563715, -0.670346220362, -0.722419247033), (0.522978400324, -0.560107588848, 0.642474187582), (-0.835312645919, -0.486739595431, 0.255611716881)-71.6580565053, 32.4137180442, -22.5226902676
2given(0.172312800159, -0.674116307989, -0.718244736984), (0.496076097592, -0.570549899365, 0.654508455051), (-0.851009285671, -0.469084230857, 0.2360999366)-71.3939296927, -13.9227702209, -33.0346346026
3given(-0.986608715419, 0.143048009287, -0.0783614043945), (0.157487494103, 0.960486043887, -0.229486924899), (0.0424373875361, -0.238754741392, -0.970152174456)1.73923189392, -12.9841119962, -101.941688245

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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.: 4
Source method: isolated from a genetically manipulated source
Details: GMP / 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: Chemical ChemComp-DGP / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.18 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

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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: 2.3→30 Å / Num. obs: 49885 / % possible obs: 93.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 33.82 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.053 / Rrim(I) all: 0.139 / Net I/σ(I): 11
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 7544 / CC1/2: 0.771 / Rpim(I) all: 0.327 / Rrim(I) all: 0.853 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.99 Å / SU ML: 0.277 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6101
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2357 2455 4.93 %
Rwork0.1834 47374 -
obs0.1859 49829 93.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.43 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9205 0 20 413 9638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00749468
X-RAY DIFFRACTIONf_angle_d0.989412871
X-RAY DIFFRACTIONf_chiral_restr0.05731400
X-RAY DIFFRACTIONf_plane_restr0.01051644
X-RAY DIFFRACTIONf_dihedral_angle_d7.06431279
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.622192908269
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.719131415948
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.688055622081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.26511430.22432725X-RAY DIFFRACTION97.78
2.34-2.390.29881630.22632688X-RAY DIFFRACTION98.01
2.39-2.440.30691390.22392742X-RAY DIFFRACTION97.89
2.44-2.50.2861350.22612722X-RAY DIFFRACTION97.78
2.5-2.560.30451560.23232702X-RAY DIFFRACTION98.15
2.56-2.630.31691470.22212746X-RAY DIFFRACTION98.3
2.63-2.710.263730.23871409X-RAY DIFFRACTION50.86
2.71-2.80.28751340.21112754X-RAY DIFFRACTION98.7
2.8-2.90.25561370.20582746X-RAY DIFFRACTION97.96
2.9-3.010.25511460.21092746X-RAY DIFFRACTION98.3
3.01-3.150.25661460.20272784X-RAY DIFFRACTION99.15
3.15-3.320.23711410.19022773X-RAY DIFFRACTION98.55
3.32-3.520.24281040.17722278X-RAY DIFFRACTION80.26
3.52-3.80.25051250.17492388X-RAY DIFFRACTION84.5
3.8-4.180.20941320.15492473X-RAY DIFFRACTION87.92
4.18-4.780.18461710.14042799X-RAY DIFFRACTION98.93
4.78-6.010.18591320.15322886X-RAY DIFFRACTION99.02
6.01-29.990.19221310.17463013X-RAY DIFFRACTION98.96

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