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- PDB-6tw4: HumRadA22F in complex with compound 6 -

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Basic information

Entry
Database: PDB / ID: 6tw4
TitleHumRadA22F in complex with compound 6
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-NZW / DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsMarsh, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,2153
Polymers26,7141
Non-polymers5012
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-12 kcal/mol
Surface area10830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.390, 60.150, 88.200
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: 26714.355 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)
Gene: radA, PF1926 / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O74036
#2: Chemical ChemComp-NZW / ~{N}-[2-[(2~{S})-2-[[(1~{S})-1-(4-methoxyphenyl)ethyl]carbamoyl]pyrrolidin-1-yl]-2-oxidanylidene-ethyl]quinoline-2-carboxamide


Mass: 460.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H28N4O4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.11 Å3/Da / Density % sol: 41.68 % / Mosaicity: 0 °
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: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2012 / Details: none
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.73→40.39 Å / Num. all: 23054 / Num. obs: 23054 / % possible obs: 99.6 % / Redundancy: 7.9 % / Biso Wilson estimate: 23.2 Å2 / Rpim(I) all: 0.035 / Rrim(I) all: 0.101 / Rsym value: 0.087 / Net I/av σ(I): 6.3 / Net I/σ(I): 15.2 / Num. measured all: 182953
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.73-1.777.81.2550.631360.5021.4331.25598.6
1.77-1.828.10.970.731080.3781.1020.9799.8
1.82-1.888.10.8260.830060.3240.9430.82698.9
1.88-1.937.80.5671.229780.2280.650.56799.3
1.93-28.30.4371.628070.1670.4920.437100
2-2.078.30.341227690.1310.3840.34199.4
2.07-2.1580.2472.826610.0960.2780.24799.6
2.15-2.237.60.1943.625740.0790.2220.194100
2.23-2.338.20.1584.424540.0610.1790.15899.9
2.33-2.4580.1265.723340.050.1450.12699.8
2.45-2.5880.1126.522450.0450.1280.11299.9
2.58-2.748.30.0937.821260.0370.1070.093100
2.74-2.928.10.0799.119990.0310.0910.079100
2.92-3.167.60.06710.218650.0280.080.067100
3.16-3.468.20.05312.516980.0220.0630.053100
3.46-3.877.70.04613.215340.0190.0550.04699.9
3.87-4.4780.0415.313530.0160.0460.0499.9
4.47-5.477.30.03616.111520.0150.0420.03699.9
5.47-7.746.90.03715.58870.0170.0450.03799.7
7.74-40.395.60.0412.74850.0210.0520.0498.4

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
BUSTER2.10.0refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J4L

5j4l


Resolution: 1.73→19.21 Å / Cor.coef. Fo:Fc: 0.9442 / Cor.coef. Fo:Fc free: 0.9304 / SU R Cruickshank DPI: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.115 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.106
RfactorNum. reflection% reflectionSelection details
Rfree0.2102 1171 5.09 %RANDOM
Rwork0.1784 ---
obs0.1801 22984 99.53 %-
Displacement parametersBiso max: 104.49 Å2 / Biso mean: 27.79 Å2 / Biso min: 10.88 Å2
Baniso -1Baniso -2Baniso -3
1-2.8635 Å20 Å20 Å2
2---4.9143 Å20 Å2
3---2.0507 Å2
Refine analyzeLuzzati coordinate error obs: 0.173 Å
Refinement stepCycle: final / Resolution: 1.73→19.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 35 143 1929
Biso mean--28.63 39.01 -
Num. residues----226
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d673SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes49HARMONIC2
X-RAY DIFFRACTIONt_gen_planes296HARMONIC5
X-RAY DIFFRACTIONt_it1842HARMONIC20
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_contact2239SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1842HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2490HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.48
X-RAY DIFFRACTIONt_other_torsion16.3
LS refinement shellResolution: 1.73→1.81 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2155 146 5.36 %
Rwork0.1913 2580 -
all0.1926 2726 -
obs--99.53 %

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