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- PDB-5xrz: Structure of a ssDNA bound to the inner DNA binding site of RAD52 -

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Basic information

Entry
Database: PDB / ID: 5xrz
TitleStructure of a ssDNA bound to the inner DNA binding site of RAD52
Components
  • DNA repair protein RAD52 homolog
  • ssDNA (40-MER)
KeywordsRECOMBINATION / Protein-DNA complex / ssDNA annealing protein / DNA repair protein
Function / homology
Function and homology information


double-strand break repair via single-strand annealing / DNA double-strand break processing involved in repair via single-strand annealing / DNA recombinase assembly / regulation of nucleotide-excision repair / mitotic recombination / HDR through MMEJ (alt-NHEJ) / HDR through Single Strand Annealing (SSA) / SUMOylation of DNA damage response and repair proteins / protein-DNA complex / double-strand break repair via homologous recombination ...double-strand break repair via single-strand annealing / DNA double-strand break processing involved in repair via single-strand annealing / DNA recombinase assembly / regulation of nucleotide-excision repair / mitotic recombination / HDR through MMEJ (alt-NHEJ) / HDR through Single Strand Annealing (SSA) / SUMOylation of DNA damage response and repair proteins / protein-DNA complex / double-strand break repair via homologous recombination / double-strand break repair / cellular response to oxidative stress / single-stranded DNA binding / DNA recombination / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
DNA repair protein Rad52/59/22 / DNA recombination/repair protein Rad52 / DNA repair protein Rad52/59/22 / Rad52 family / DNA repair protein Rad52/59/22 superfamily / Rad52/22 family double-strand break repair protein / Enolase-like; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA repair protein RAD52 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsSaotome, M. / Saito, K. / Yasuda, T. / Sugiyama, S. / Kurumizaka, H. / Kagawa, W.
Funding support Japan, 4items
OrganizationGrant numberCountry
JSPS KAKENHIJP24570138 Japan
JSPS KAKENHIJP26116521 Japan
JSPS KAKENHIJP16H01316 Japan
Japan Private School Promotion Foundation Japan
CitationJournal: iScience / Year: 2018
Title: Structural Basis of Homology-Directed DNA Repair Mediated by RAD52
Authors: Saotome, M. / Saito, K. / Yasuda, T. / Ohtomo, H. / Sugiyama, S. / Nishimura, Y. / Kurumizaka, H. / Kagawa, W.
History
DepositionJun 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair protein RAD52 homolog
B: DNA repair protein RAD52 homolog
C: DNA repair protein RAD52 homolog
D: DNA repair protein RAD52 homolog
E: DNA repair protein RAD52 homolog
F: DNA repair protein RAD52 homolog
G: DNA repair protein RAD52 homolog
H: DNA repair protein RAD52 homolog
I: DNA repair protein RAD52 homolog
J: DNA repair protein RAD52 homolog
K: DNA repair protein RAD52 homolog
L: ssDNA (40-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,04222
Polymers271,65112
Non-polymers39110
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area77500 Å2
ΔGint-326 kcal/mol
Surface area74710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.621, 101.420, 101.710
Angle α, β, γ (deg.)91.89, 108.68, 108.17
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
DNA repair protein RAD52 homolog /


Mass: 23597.582 Da / Num. of mol.: 11 / Fragment: UNP residues 1-212 / Mutation: K102A, K133A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD52 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P43351
#2: DNA chain ssDNA (40-MER)


Mass: 12077.721 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K

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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: 2.29 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: calcium acetate, PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 7, 2014
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.6→95.3 Å / Num. obs: 27023 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 100.2 Å2 / CC1/2: 0.972 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.103 / Rrim(I) all: 0.145 / Rsym value: 0.103 / Net I/σ(I): 7.5
Reflection shellResolution: 3.6→3.7 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4412 / CC1/2: 0.597 / Rpim(I) all: 0.4 / Rrim(I) all: 0.565 / Rsym value: 0.103 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KN0

1kn0


Resolution: 3.6→45.703 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 31.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2565 1430 5.3 %
Rwork0.2165 --
obs0.2188 26956 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→45.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15862 794 10 0 16666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216999
X-RAY DIFFRACTIONf_angle_d0.4823049
X-RAY DIFFRACTIONf_dihedral_angle_d8.5410109
X-RAY DIFFRACTIONf_chiral_restr0.0392458
X-RAY DIFFRACTIONf_plane_restr0.0042922
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6001-3.72870.31981430.29812576X-RAY DIFFRACTION97
3.7287-3.8780.30021400.26282537X-RAY DIFFRACTION97
3.878-4.05440.2633990.2592622X-RAY DIFFRACTION97
4.0544-4.2680.28461360.22422548X-RAY DIFFRACTION96
4.268-4.53510.24221470.20832518X-RAY DIFFRACTION97
4.5351-4.88490.26141630.19192577X-RAY DIFFRACTION98
4.8849-5.37580.26021450.21132548X-RAY DIFFRACTION97
5.3758-6.15210.28261720.21982504X-RAY DIFFRACTION96
6.1521-7.74490.22971410.21172536X-RAY DIFFRACTION96
7.7449-45.70720.22491440.18712560X-RAY DIFFRACTION97

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