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- PDB-9ee7: Folded domains of Xrs2 from S.cerevisiae -

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Basic information

Entry
Database: PDB / ID: 9ee7
TitleFolded domains of Xrs2 from S.cerevisiae
ComponentsDNA repair protein XRS2
KeywordsPROTEIN BINDING / DNA repair
Function / homology
Function and homology information


mitochondrial double-strand break repair via homologous recombination / Mre11 complex / meiotic DNA double-strand break formation / R-loop processing / maintenance of DNA trinucleotide repeats / double-stranded telomeric DNA binding / G-quadruplex DNA binding / single-stranded telomeric DNA binding / sporulation resulting in formation of a cellular spore / telomeric DNA binding ...mitochondrial double-strand break repair via homologous recombination / Mre11 complex / meiotic DNA double-strand break formation / R-loop processing / maintenance of DNA trinucleotide repeats / double-stranded telomeric DNA binding / G-quadruplex DNA binding / single-stranded telomeric DNA binding / sporulation resulting in formation of a cellular spore / telomeric DNA binding / telomere maintenance / base-excision repair / double-strand break repair via nonhomologous end joining / double-strand break repair / protein-macromolecule adaptor activity / chromosome, telomeric region / DNA binding / nucleoplasm / nucleus
Similarity search - Function
FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily
Similarity search - Domain/homology
DNA repair protein XRS2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsVigneswaran, A. / Shi, K. / Evans, R. / Aihara, H. / Latham, M.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128906 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Crystal structure of the folded domains of Xrs2 from Saccharomyces cerevisiae.
Authors: Vigneswaran, A. / Shi, K. / Aihara, H. / Evans 3rd, R.L. / Latham, M.P.
History
DepositionNov 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA repair protein XRS2


Theoretical massNumber of molelcules
Total (without water)37,1731
Polymers37,1731
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.843, 84.843, 316.716
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein DNA repair protein XRS2


Mass: 37172.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: XRS2, YDR369C, D9481.13 / Production host: Escherichia coli (E. coli) / References: UniProt: P33301
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 4.43 Å3/Da / Density % sol: 72.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 3.0 M NaCl, 0.1M Tris, pH 8.3 / Temp details: At room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.38→71.58 Å / Num. obs: 27755 / % possible obs: 100 % / Redundancy: 21.7 % / Biso Wilson estimate: 74.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.031 / Rsym value: 0.144 / Net I/σ(I): 16.4
Reflection shellResolution: 2.38→2.434 Å / Rmerge(I) obs: 3.608 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1350 / CC1/2: 0.444 / Rpim(I) all: 0.82 / Rrim(I) all: 3.701 / Rsym value: 3.608

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→71.58 Å / SU ML: 0.5256 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 45.251
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.3115 1284 5.03 %RANDOM
Rwork0.2981 24252 --
obs0.2987 25536 90.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.24 Å2
Refinement stepCycle: LAST / Resolution: 2.38→71.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2176 0 0 7 2183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00862218
X-RAY DIFFRACTIONf_angle_d1.12013039
X-RAY DIFFRACTIONf_chiral_restr0.0584378
X-RAY DIFFRACTIONf_plane_restr0.0085382
X-RAY DIFFRACTIONf_dihedral_angle_d6.9316311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.470.4405500.4362939X-RAY DIFFRACTION32.42
2.47-2.580.45561300.44232307X-RAY DIFFRACTION79.33
2.58-2.720.43851380.40462901X-RAY DIFFRACTION99.25
2.72-2.890.42251490.40512908X-RAY DIFFRACTION99.32
2.89-3.110.51271490.42782940X-RAY DIFFRACTION99.42
3.11-3.430.3951770.37042932X-RAY DIFFRACTION99.68
3.43-3.920.34911490.30433011X-RAY DIFFRACTION99.94
3.93-4.940.25651640.24743038X-RAY DIFFRACTION99.91
4.94-71.580.26221780.26633276X-RAY DIFFRACTION100

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