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- PDB-7qv8: Leishmania infantum BRC1 repeat in complex with LiRAD51 -

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Basic information

Entry
Database: PDB / ID: 7qv8
TitleLeishmania infantum BRC1 repeat in complex with LiRAD51
Components
  • DNA repair protein RAD51 homolog
  • DNA_repair_protein_BRCA2_-_putative
KeywordsRECOMBINATION / BRC repeat / homologous recombination / Rad51 / recombinase. BRCA2
Function / homology
Function and homology information


mitotic recombination-dependent replication fork processing / DNA strand exchange activity / ATP-dependent activity, acting on DNA / double-strand break repair via homologous recombination / single-stranded DNA binding / double-stranded DNA binding / ATP binding / nucleus
Similarity search - Function
Rad51/DMC1/RadA / BRCA2 repeat / BRCA2, OB1 / Breast cancer type 2 susceptibility protein / BRCA2 repeat / BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 / BRCA2 repeat profile. / DNA recombination/repair protein Rad51 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal ...Rad51/DMC1/RadA / BRCA2 repeat / BRCA2, OB1 / Breast cancer type 2 susceptibility protein / BRCA2 repeat / BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 / BRCA2 repeat profile. / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Uncharacterized protein / DNA repair protein RAD51 homolog
Similarity search - Component
Biological speciesLeishmania infantum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsPantelejevs, T. / Hyvonen, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Biochem.J. / Year: 2022
Title: Divergent binding mode for a protozoan BRC repeat to RAD51.
Authors: Pantelejevs, T. / Hyvonen, M.
History
DepositionJan 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: 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

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Assembly

Deposited unit
A: DNA repair protein RAD51 homolog
D: DNA_repair_protein_BRCA2_-_putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9504
Polymers28,4982
Non-polymers4522
Water84747
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-29 kcal/mol
Surface area10750 Å2
Unit cell
Length a, b, c (Å)61.004, 61.004, 119.224
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein DNA repair protein RAD51 homolog /


Mass: 24838.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: RAD51, LINF_280010500, LINJ_28_0580 / Production host: Escherichia coli (E. coli) / References: UniProt: A4I3C9
#2: Protein/peptide DNA_repair_protein_BRCA2_-_putative


Mass: 3660.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: LINF_200005600, LINJ_20_0070 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4HYJ9
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 36.8 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 32% low-PEG-smear, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: LN2 stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.15→59.61 Å / Num. obs: 12826 / % possible obs: 98.9 % / Redundancy: 23.1 % / Biso Wilson estimate: 57.32 Å2 / CC1/2: 1 / Net I/σ(I): 15.6
Reflection shellResolution: 2.15→2.18 Å / Redundancy: 18.1 % / Num. unique obs: 632 / CC1/2: 0.5 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N0W

1n0w


Resolution: 2.15→54.31 Å / SU ML: 0.4145 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 45.579
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3056 603 4.99 %
Rwork0.2778 11482 -
obs0.2791 12085 93.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.53 Å2
Refinement stepCycle: LAST / Resolution: 2.15→54.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 28 47 1837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01241811
X-RAY DIFFRACTIONf_angle_d1.51362450
X-RAY DIFFRACTIONf_chiral_restr0.098288
X-RAY DIFFRACTIONf_plane_restr0.0026313
X-RAY DIFFRACTIONf_dihedral_angle_d11.4794664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.360.44471390.43272229X-RAY DIFFRACTION75.41
2.37-2.710.38891630.34692979X-RAY DIFFRACTION98.96
2.71-3.410.3731400.33113051X-RAY DIFFRACTION99.53
3.41-54.310.26531610.24523223X-RAY DIFFRACTION99.85

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