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- PDB-3lda: Yeast Rad51 H352Y Filament Interface Mutant -

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Basic information

Entry
Database: PDB / ID: 3lda
TitleYeast Rad51 H352Y Filament Interface Mutant
ComponentsDNA repair protein RAD51
KeywordsDNA BINDING PROTEIN / ATP-binding / DNA damage / DNA recombination / DNA repair / Nucleotide-binding / non-prolyl cis peptide / ATP-hydrolysis / Walker A/B
Function / homology
Function and homology information


Presynaptic phase of homologous DNA pairing and strand exchange / heteroduplex formation / meiotic joint molecule formation / mitochondrial chromosome / mitotic recombination-dependent replication fork processing / chromosome organization involved in meiotic cell cycle / DNA recombinase assembly / DNA strand invasion / mitotic recombination / DNA strand exchange activity ...Presynaptic phase of homologous DNA pairing and strand exchange / heteroduplex formation / meiotic joint molecule formation / mitochondrial chromosome / mitotic recombination-dependent replication fork processing / chromosome organization involved in meiotic cell cycle / DNA recombinase assembly / DNA strand invasion / mitotic recombination / DNA strand exchange activity / telomere maintenance via recombination / reciprocal meiotic recombination / ATP-dependent DNA damage sensor activity / mitochondrial DNA repair / nuclear chromosome / ATP-dependent activity, acting on DNA / condensed nuclear chromosome / nucleotide-excision repair / double-strand break repair via homologous recombination / G2/M transition of mitotic cell cycle / double-strand break repair / single-stranded DNA binding / double-stranded DNA binding / DNA recombination / mitochondrial matrix / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding
Similarity search - Function
DNA recombination/repair protein Rad51 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain ...DNA recombination/repair protein Rad51 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA repair protein RAD51
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVillanueva, N.L. / Chen, J. / Morrical, S.W. / Rould, M.A.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Insights into the mechanism of Rad51 recombinase from the structure and properties of a filament interface mutant.
Authors: Chen, J. / Villanueva, N. / Rould, M.A. / Morrical, S.W.
History
DepositionJan 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair protein RAD51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1394
Polymers43,0321
Non-polymers1063
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.905, 78.905, 130.333
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsA SINGLE TURN HELICAL FILAMENT CAN BE FORMED BY APPLYING SYMMETRY OPERATION 2_555 WITH TRANSLATION (118.35755, -68.33369, -86.88798), 3_555 WITH (118.35751, 68.33368, -43.44404), 4_555 WITH (157.80998, 0, -65.16603), 5_555 WITH (39.45252, 68.33371, -21.722), AND 6_555 WITH (39.45249,-68.33371,-108.61001)

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Components

#1: Protein DNA repair protein RAD51


Mass: 43032.355 Da / Num. of mol.: 1 / Mutation: H352Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RAD51, YER095W / Production host: Escherichia coli (E. coli) / References: UniProt: P25454
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 35% (v/v) Pentaerythritol propoxylate (5/4 PO/OH), 300mM KCl, 50mM HEPES, 20mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03320357 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 28, 2008
Details: Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03320357 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 15930 / Num. obs: 14791 / % possible obs: 92.8 % / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 56.2 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 18.03
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 2.03 / % possible all: 98.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
EPMRphasing
CNS1.21refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SZP

1szp


Resolution: 2.5→50 Å / Isotropic thermal model: anisotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 1495 -Random
Rwork0.2003 ---
all-15930 --
obs-14791 92.8 %-
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 3 79 2314
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006256
X-RAY DIFFRACTIONc_angle_deg1.34652

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