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- PDB-5xs0: Structure of a ssDNA bound to the outer DNA binding site of RAD52 -

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Basic information

Entry
Database: PDB / ID: 5xs0
TitleStructure of a ssDNA bound to the outer DNA binding site of RAD52
Components
  • DNA repair protein RAD52 homolog
  • ssDNA (5'-D(*CP*CP*CP*CP*CP*C)-3')
  • ssDNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*C)-3')
  • ssDNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')
  • ssDNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')
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 / mitotic recombination / regulation of nucleotide-excision repair / 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 / mitotic recombination / regulation of nucleotide-excision repair / 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 / single-stranded DNA binding / cellular response to oxidative stress / 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 repair protein RAD52 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSaotome, M. / Saito, K. / Yasuda, T. / Sugiyama, S. / Kurumizaka, H. / Kagawa, W.
Funding support Japan, 7items
OrganizationGrant numberCountry
JSPS KAKENHIJP24570138 Japan
JSPS KAKENHIJP26116521 Japan
JSPS KAKENHIJP16H01316 Japan
JSPS KAKENHIJP25116002 Japan
JSPS KAKENHIJP25250023 Japan
JSPS KAKENHIJP17H01408 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: DNA repair protein RAD52 homolog
M: DNA repair protein RAD52 homolog
N: DNA repair protein RAD52 homolog
O: DNA repair protein RAD52 homolog
P: DNA repair protein RAD52 homolog
Q: DNA repair protein RAD52 homolog
R: DNA repair protein RAD52 homolog
S: DNA repair protein RAD52 homolog
T: DNA repair protein RAD52 homolog
U: DNA repair protein RAD52 homolog
V: DNA repair protein RAD52 homolog
W: ssDNA (5'-D(*CP*CP*CP*CP*CP*C)-3')
X: ssDNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*C)-3')
Y: ssDNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')
Z: ssDNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)531,06626
Polymers531,06626
Non-polymers00
Water0
1
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
Y: ssDNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')

Z: ssDNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)266,25613
Polymers266,25613
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,y+1/2,-z-11
Buried area63010 Å2
ΔGint-245 kcal/mol
Surface area81650 Å2
MethodPISA
2
L: DNA repair protein RAD52 homolog
M: DNA repair protein RAD52 homolog
N: DNA repair protein RAD52 homolog
O: DNA repair protein RAD52 homolog
P: DNA repair protein RAD52 homolog
Q: DNA repair protein RAD52 homolog
R: DNA repair protein RAD52 homolog
S: DNA repair protein RAD52 homolog
T: DNA repair protein RAD52 homolog
U: DNA repair protein RAD52 homolog
V: DNA repair protein RAD52 homolog
W: ssDNA (5'-D(*CP*CP*CP*CP*CP*C)-3')
X: ssDNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)264,81013
Polymers264,81013
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area62620 Å2
ΔGint-245 kcal/mol
Surface area81210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.224, 164.408, 166.087
Angle α, β, γ (deg.)90.00, 90.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ...
DNA repair protein RAD52 homolog /


Mass: 23713.785 Da / Num. of mol.: 22 / Fragment: UNP residues 1-212
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 (5'-D(*CP*CP*CP*CP*CP*C)-3')


Mass: 1690.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain ssDNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*C)-3')


Mass: 2268.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain ssDNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')


Mass: 2846.861 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain ssDNA (5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*C)-3')


Mass: 2557.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / Details: lithium citrate, PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2011
RadiationMonochromator: NUMERICAL LINK TYPE SI(111) DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→48.63 Å / Num. obs: 107806 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 91 Å2 / CC1/2: 0.997 / Rsym value: 0.083 / Net I/σ(I): 11.8
Reflection shellResolution: 3→3.05 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5281 / CC1/2: 0.733 / Rsym value: 0.686 / % possible all: 98.7

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Processing

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

1kn0


Resolution: 3→48.529 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2506 5188 4.83 %
Rwork0.221 --
obs0.2225 107485 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→48.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31852 615 0 0 32467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00333055
X-RAY DIFFRACTIONf_angle_d0.57144554
X-RAY DIFFRACTIONf_dihedral_angle_d13.60819898
X-RAY DIFFRACTIONf_chiral_restr0.0434720
X-RAY DIFFRACTIONf_plane_restr0.0045803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.03410.35251560.31363403X-RAY DIFFRACTION98
3.0341-3.06980.3311520.30423390X-RAY DIFFRACTION100
3.0698-3.10720.35162060.30293357X-RAY DIFFRACTION100
3.1072-3.14660.33691990.29563401X-RAY DIFFRACTION100
3.1466-3.18790.33251500.29453374X-RAY DIFFRACTION100
3.1879-3.23160.30511550.293460X-RAY DIFFRACTION100
3.2316-3.27780.31571300.27713407X-RAY DIFFRACTION100
3.2778-3.32670.35961560.27593421X-RAY DIFFRACTION100
3.3267-3.37870.27491830.26683392X-RAY DIFFRACTION100
3.3787-3.4340.29721870.25683399X-RAY DIFFRACTION100
3.434-3.49320.29721710.25653399X-RAY DIFFRACTION100
3.4932-3.55670.30571570.24813392X-RAY DIFFRACTION100
3.5567-3.62510.30731850.2573418X-RAY DIFFRACTION100
3.6251-3.69910.29461940.25273388X-RAY DIFFRACTION100
3.6991-3.77950.27721390.23663415X-RAY DIFFRACTION100
3.7795-3.86740.27841530.23783448X-RAY DIFFRACTION100
3.8674-3.96410.28181710.22413382X-RAY DIFFRACTION100
3.9641-4.07120.27862070.24223353X-RAY DIFFRACTION100
4.0712-4.19090.24391620.21443468X-RAY DIFFRACTION100
4.1909-4.32610.21861780.19753396X-RAY DIFFRACTION100
4.3261-4.48060.24521460.19353427X-RAY DIFFRACTION100
4.4806-4.65990.20611940.18263378X-RAY DIFFRACTION100
4.6599-4.87180.21291590.18153429X-RAY DIFFRACTION100
4.8718-5.12840.21421760.19233412X-RAY DIFFRACTION100
5.1284-5.44930.21922060.19113383X-RAY DIFFRACTION100
5.4493-5.86930.19331880.19463435X-RAY DIFFRACTION100
5.8693-6.45880.2511470.21963454X-RAY DIFFRACTION100
6.4588-7.39060.22732270.19113362X-RAY DIFFRACTION100
7.3906-9.30060.19841830.18373463X-RAY DIFFRACTION100
9.3006-48.53570.21411710.19873491X-RAY DIFFRACTION100

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