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- PDB-5jrb: Rad52(1-212) K102A/K133A/E202A mutant -

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Basic information

Entry
Database: PDB / ID: 5jrb
TitleRad52(1-212) K102A/K133A/E202A mutant
ComponentsDNA repair protein RAD52 homolog
KeywordsDNA BINDING PROTEIN / DNA annealing protein / ssDNA binding / multimeric ring formation
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 repair protein RAD52 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.405 Å
AuthorsSaotome, M. / Saito, K. / Kurumizaka, H. / Kagawa, W.
Funding support Japan, 3items
OrganizationGrant numberCountry
JSPS KAKENHI24570138 Japan
MEXT KAKENHI26116521 Japan
MEXT KAKENHI25116002 Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Structure of the human DNA-repair protein RAD52 containing surface mutations.
Authors: Saotome, M. / Saito, K. / Onodera, K. / Kurumizaka, H. / Kagawa, W.
History
DepositionMay 6, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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


Theoretical massNumber of molelcules
Total (without water)258,93511
Polymers258,93511
Non-polymers00
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59590 Å2
ΔGint-233 kcal/mol
Surface area82680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.955, 98.516, 116.367
Angle α, β, γ (deg.)90.00, 91.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA repair protein RAD52 homolog /


Mass: 23539.547 Da / Num. of mol.: 11 / Fragment: UNP residues 1-212 / Mutation: K102A, K133A, E202A
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.05M Sodium malonate pH6.0, 5% PEG 3350

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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 270 / Detector: CCD / Date: Dec 15, 2015
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→49.3 Å / Num. obs: 190708 / % possible obs: 99.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 49.4 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.095 / Net I/σ(I): 9.2
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 1.9 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1kn0

1kn0


Resolution: 2.405→49.258 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0.95 / Phase error: 30.13 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2731 9527 5 %
Rwork0.2237 --
obs0.2261 190634 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.405→49.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15852 0 0 400 16252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816117
X-RAY DIFFRACTIONf_angle_d1.01821695
X-RAY DIFFRACTIONf_dihedral_angle_d15.1439705
X-RAY DIFFRACTIONf_chiral_restr0.0552303
X-RAY DIFFRACTIONf_plane_restr0.0072878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4048-2.43210.3363080.32975810X-RAY DIFFRACTION96
2.4321-2.46070.32593190.30466070X-RAY DIFFRACTION100
2.4607-2.49080.3233140.29315973X-RAY DIFFRACTION100
2.4908-2.52230.32493220.28076079X-RAY DIFFRACTION100
2.5223-2.55550.31673190.29476095X-RAY DIFFRACTION100
2.5555-2.59050.36383250.29486116X-RAY DIFFRACTION100
2.5905-2.62750.33553180.29555975X-RAY DIFFRACTION100
2.6275-2.66670.33463120.28995996X-RAY DIFFRACTION99
2.6667-2.70840.34843130.28966004X-RAY DIFFRACTION99
2.7084-2.75280.35413180.27826086X-RAY DIFFRACTION100
2.7528-2.80020.3243190.27966061X-RAY DIFFRACTION100
2.8002-2.85110.37943150.26996027X-RAY DIFFRACTION100
2.8511-2.9060.3243200.2516117X-RAY DIFFRACTION100
2.906-2.96530.28193220.26386015X-RAY DIFFRACTION100
2.9653-3.02980.3093210.26196063X-RAY DIFFRACTION100
3.0298-3.10020.3153210.276069X-RAY DIFFRACTION100
3.1002-3.17770.29413170.24326051X-RAY DIFFRACTION100
3.1777-3.26360.2823170.23616015X-RAY DIFFRACTION100
3.2636-3.35970.29933200.23846085X-RAY DIFFRACTION100
3.3597-3.46810.30253190.24236009X-RAY DIFFRACTION99
3.4681-3.5920.25743180.22566023X-RAY DIFFRACTION100
3.592-3.73580.28873160.22186045X-RAY DIFFRACTION100
3.7358-3.90570.23413250.20216068X-RAY DIFFRACTION100
3.9057-4.11150.28113160.20746051X-RAY DIFFRACTION100
4.1115-4.3690.22553140.18536010X-RAY DIFFRACTION100
4.369-4.70610.22323190.18586031X-RAY DIFFRACTION100
4.7061-5.17920.25033140.19286085X-RAY DIFFRACTION100
5.1792-5.92760.23443120.18536031X-RAY DIFFRACTION100
5.9276-7.46390.21273160.18356036X-RAY DIFFRACTION99
7.4639-49.26830.22223180.16736011X-RAY DIFFRACTION99

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