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- PDB-1h2i: Human Rad52 protein, N-terminal domain -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1h2i
TitleHuman Rad52 protein, N-terminal domain
ComponentsDNA REPAIR PROTEIN RAD52 HOMOLOG
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / DNA REPAIR / DNA RECOMBINATION
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 / MIRAS / Resolution: 2.7 Å
AuthorsSingleton, M.R. / Wentzell, L.M. / Liu, Y. / West, S.C. / Wigley, D.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structure of the Single-Strand Annealing Domain of Human Rad52 Protein
Authors: Singleton, M.R. / Wentzell, L.M. / Liu, Y. / West, S.C. / Wigley, D.B.
History
DepositionAug 9, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)507,96022
Polymers507,96022
Non-polymers00
Water8,719484
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


Theoretical massNumber of molelcules
Total (without water)253,98011
Polymers253,98011
Non-polymers00
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
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


Theoretical massNumber of molelcules
Total (without water)253,98011
Polymers253,98011
Non-polymers00
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)117.259, 127.319, 191.227
Angle α, β, γ (deg.)90.00, 90.29, 90.00
Int Tables number4
Space group name H-MP1211
DetailsCHAINS A-K FORM ONE UNDECAMERIC UNITCHAINS L-V FORM ONE UNDECAMERIC UNIT

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Components

#1: Protein ...
DNA REPAIR PROTEIN RAD52 HOMOLOG / / RAD52


Mass: 23089.096 Da / Num. of mol.: 22 / Fragment: DNA-BINDING DOMAIN, RESIDUES 1-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P43351
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 484 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINVOLVED IN DOUBLE-STRANDED BREAK REPAIR
Sequence detailsSTRUCTURE IS OF N-TERMINAL DOMAIN, RESIDUES 1-209

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growpH: 8 / Details: pH 8.00
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMTris-HCl1droppH7.5
3300 mM1dropNaCl
41 mMdithiothreitol1drop
5100 mMTris-HCl1reservoirpH8.0
64-14 %(v/v)ethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 149457 / % possible obs: 97 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 14
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 2.7 / % possible all: 96.7
Reflection
*PLUS
Lowest resolution: 30 Å
Reflection shell
*PLUS
% possible obs: 96.7 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.7→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 -5 %RANDOM
Rwork0.225 ---
obs0.225 149457 96.9 %-
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32318 0 0 484 32802
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.78
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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