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- PDB-6tw9: HumRadA22F in complex with CAM833 -

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Basic information

Entry
Database: PDB / ID: 6tw9
TitleHumRadA22F in complex with CAM833
ComponentsDNA repair and recombination protein RadA
KeywordsDNA BINDING PROTEIN / RAD51 / RECOMBINASE / DNA REPAIR
Function / homology
Function and homology information


ATP-dependent DNA damage sensor activity / DNA recombination / damaged DNA binding / DNA repair / ATP hydrolysis activity / ATP binding
Similarity search - Function
DNA recombination/repair protein RadA / 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 RadA / 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 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-O08 / DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsFischer, G. / Marsh, M.E. / Scott, D.E. / Coyne, A.G. / Skidmore, J. / Abell, C. / Hyvonen, M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust91050/Z/10/Z United Kingdom
Wellcome Trust080083/Z/06/Z United Kingdom
CitationJournal: Cell Chem Biol / Year: 2021
Title: A small-molecule inhibitor of the BRCA2-RAD51 interaction modulates RAD51 assembly and potentiates DNA damage-induced cell death.
Authors: Scott, D.E. / Francis-Newton, N.J. / Marsh, M.E. / Coyne, A.G. / Fischer, G. / Moschetti, T. / Bayly, A.R. / Sharpe, T.D. / Haas, K.T. / Barber, L. / Valenzano, C.R. / Srinivasan, R. / ...Authors: Scott, D.E. / Francis-Newton, N.J. / Marsh, M.E. / Coyne, A.G. / Fischer, G. / Moschetti, T. / Bayly, A.R. / Sharpe, T.D. / Haas, K.T. / Barber, L. / Valenzano, C.R. / Srinivasan, R. / Huggins, D.J. / Lee, M. / Emery, A. / Hardwick, B. / Ehebauer, M. / Dagostin, C. / Esposito, A. / Pellegrini, L. / Perrior, T. / McKenzie, G. / Blundell, T.L. / Hyvonen, M. / Skidmore, J. / Venkitaraman, A.R. / Abell, C.
History
DepositionJan 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 30, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: DNA repair and recombination protein RadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0604
Polymers25,3991
Non-polymers6613
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-12 kcal/mol
Surface area10850 Å2
Unit cell
Length a, b, c (Å)40.376, 61.213, 87.678
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA repair and recombination protein RadA


Mass: 25398.896 Da / Num. of mol.: 1 / Fragment: humRadA22F
Mutation: S167K, V168A, I169M, W170Y, N175G, I182L, R183L, D192S, P193G D194S, E195D, K198D, H199N, I200V, Y201A, V202Y, L213Q, V215L, Q216Y, E219S, D220A, K221M, I222M, K223V, L225S, V232Y, K263R, ...Mutation: S167K, V168A, I169M, W170Y, N175G, I182L, R183L, D192S, P193G D194S, E195D, K198D, H199N, I200V, Y201A, V202Y, L213Q, V215L, Q216Y, E219S, D220A, K221M, I222M, K223V, L225S, V232Y, K263R, H264F, A266R, D267M, L274E, Y275F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: radA, PF1926 / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O74036
#2: Chemical ChemComp-O08 / ~{N}-[2-[(2~{S},4~{R})-2-[[(1~{S})-1-(2-chloranyl-4-methoxy-phenyl)ethyl]carbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-2-oxidanylidene-ethyl]-6-fluoranyl-quinoline-2-carboxamide


Mass: 528.960 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H26ClFN4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 20% PEG8000, 0.08 M Na Cacodylate pH 6.5, 0.16M Ca acetate, 18% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2013 / Details: none
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.517→61.213 Å / Num. obs: 32571 / % possible obs: 94.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 15.19 Å2 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.043 / Rrim(I) all: 0.098 / Net I/σ(I): 12.5 / Num. measured all: 149322
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsRpim(I) allRrim(I) all% possible all
1.517-1.5224.60.6723510.3380.75697.5
7.037-61.2134.40.0223460.0110.02584.4

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Processing

Software
NameVersionClassification
Aimlessdata scaling
BUSTER2.11.4refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J4L

5j4l


Resolution: 1.52→50.19 Å / Cor.coef. Fo:Fc: 0.9585 / Cor.coef. Fo:Fc free: 0.9563 / SU R Cruickshank DPI: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.073 / SU Rfree Blow DPI: 0.068 / SU Rfree Cruickshank DPI: 0.067
RfactorNum. reflection% reflectionSelection details
Rfree0.1716 1634 5.05 %RANDOM
Rwork0.1563 ---
obs0.1571 32329 94.44 %-
Displacement parametersBiso max: 82.11 Å2 / Biso mean: 16.97 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-0.7386 Å20 Å20 Å2
2---2.4565 Å20 Å2
3---1.7179 Å2
Refinement stepCycle: final / Resolution: 1.52→50.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 44 258 2039
Biso mean--19.11 30.61 -
Num. residues----224
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d832SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes586HARMONIC5
X-RAY DIFFRACTIONt_it3649HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion239SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4346SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3649HARMONIC20.011
X-RAY DIFFRACTIONt_angle_deg6604HARMONIC21.16
X-RAY DIFFRACTIONt_omega_torsion4.11
X-RAY DIFFRACTIONt_other_torsion16.05
LS refinement shellResolution: 1.52→1.57 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2234 171 5.64 %
Rwork0.1932 2859 -
all0.1948 3030 -
obs--94.44 %

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