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- PDB-6wcd: Crystal Structure of Xenopus laevis APE2 Catalytic Domain -

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Basic information

Entry
Database: PDB / ID: 6wcd
TitleCrystal Structure of Xenopus laevis APE2 Catalytic Domain
ComponentsDNA-(apurinic or apyrimidinic site) lyase
KeywordsHYDROLASE / nuclease / DNA repair
Function / homology
Function and homology information


exodeoxyribonuclease III / chromosome / endonuclease activity / DNA repair / mitochondrion / DNA binding / zinc ion binding / nucleus
Similarity search - Function
Zinc finger, GRF-type / GRF zinc finger / Zinc finger GRF-type profile. / 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
1,4-BUTANEDIOL / DNA-(apurinic or apyrimidinic site) endonuclease 2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsWojtaszek, J.L. / Wallace, B.D. / Williams, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1Z01ES102765 United States
CitationJournal: Mol.Cell / Year: 2020
Title: Endogenous DNA 3' Blocks Are Vulnerabilities for BRCA1 and BRCA2 Deficiency and Are Reversed by the APE2 Nuclease.
Authors: Alvarez-Quilon, A. / Wojtaszek, J.L. / Mathieu, M.C. / Patel, T. / Appel, C.D. / Hustedt, N. / Rossi, S.E. / Wallace, B.D. / Setiaputra, D. / Adam, S. / Ohashi, Y. / Melo, H. / Cho, T. / ...Authors: Alvarez-Quilon, A. / Wojtaszek, J.L. / Mathieu, M.C. / Patel, T. / Appel, C.D. / Hustedt, N. / Rossi, S.E. / Wallace, B.D. / Setiaputra, D. / Adam, S. / Ohashi, Y. / Melo, H. / Cho, T. / Gervais, C. / Munoz, I.M. / Grazzini, E. / Young, J.T.F. / Rouse, J. / Zinda, M. / Williams, R.S. / Durocher, D.
History
DepositionMar 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 1, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 18, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-(apurinic or apyrimidinic site) lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4087
Polymers39,8561
Non-polymers5526
Water6,269348
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.383, 73.149, 98.877
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

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA-(apurinic or apyrimidinic site) lyase / APE2


Mass: 39855.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: apex2, apex2-prov / Production host: Escherichia coli (E. coli)
References: UniProt: Q6DDT4, DNA-(apurinic or apyrimidinic site) lyase

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Non-polymers , 5 types, 354 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 6000, 0.1 M MES pH 6.5, 2:1 and 1:1 protein:crystallant ratios

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→37.17 Å / Num. obs: 60632 / % possible obs: 99.34 % / Redundancy: 5.3 % / Rrim(I) all: 0.084 / Net I/σ(I): 16.14
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 4.2 % / Num. unique obs: 5767 / Rrim(I) all: 0.477 / % possible all: 94.99

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G0R

3g0r


Resolution: 1.54→37.17 Å / SU ML: 0.1144 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.5959
RfactorNum. reflection% reflection
Rfree0.157 3074 5.07 %
Rwork0.1433 --
obs0.144 60632 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.94 Å2
Refinement stepCycle: LAST / Resolution: 1.54→37.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2465 0 30 348 2843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01412607
X-RAY DIFFRACTIONf_angle_d1.34563539
X-RAY DIFFRACTIONf_chiral_restr0.0783388
X-RAY DIFFRACTIONf_plane_restr0.01463
X-RAY DIFFRACTIONf_dihedral_angle_d18.4206984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.570.2241340.23152348X-RAY DIFFRACTION89.99
1.57-1.590.21041400.18452552X-RAY DIFFRACTION98.93
1.59-1.620.17171400.1762610X-RAY DIFFRACTION100
1.62-1.650.20771320.16782598X-RAY DIFFRACTION99.71
1.65-1.680.17981380.15992586X-RAY DIFFRACTION99.82
1.68-1.710.18151290.15812613X-RAY DIFFRACTION99.93
1.71-1.750.16541510.15452567X-RAY DIFFRACTION99.89
1.75-1.790.18551520.15272588X-RAY DIFFRACTION99.96
1.79-1.840.17121270.13922656X-RAY DIFFRACTION99.93
1.84-1.890.16011230.13482610X-RAY DIFFRACTION100
1.89-1.940.13171430.13472628X-RAY DIFFRACTION99.93
1.94-20.16881440.13132591X-RAY DIFFRACTION99.96
2-2.080.14641530.13152606X-RAY DIFFRACTION100
2.08-2.160.15391290.13172648X-RAY DIFFRACTION99.96
2.16-2.260.15491400.13252623X-RAY DIFFRACTION99.96
2.26-2.380.14121410.12792638X-RAY DIFFRACTION99.96
2.38-2.530.16021430.13472628X-RAY DIFFRACTION99.96
2.53-2.720.1441420.13562644X-RAY DIFFRACTION99.86
2.72-2.990.15511510.14352659X-RAY DIFFRACTION99.89
2.99-3.430.16971370.14462680X-RAY DIFFRACTION99.93
3.43-4.320.12911480.13082691X-RAY DIFFRACTION99.79
4.32-37.170.16631370.15972794X-RAY DIFFRACTION97.93

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