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- PDB-6tw3: HumRadA2 in complex with Naphthyl-HPA fragment-peptide chimera -

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Basic information

Entry
Database: PDB / ID: 6tw3
TitleHumRadA2 in complex with Naphthyl-HPA fragment-peptide chimera
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-O0E / PHOSPHATE ION / DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.352 Å
AuthorsMarsh, M.E. / Fischer, G. / 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 1.1Apr 7, 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)26,1844
Polymers25,5021
Non-polymers6813
Water6,449358
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-12 kcal/mol
Surface area11240 Å2
Unit cell
Length a, b, c (Å)40.526, 61.949, 87.724
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: 25502.150 Da / Num. of mol.: 1
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-O0E / (2~{S})-1-[(2~{S})-2-[(3-azanylnaphthalen-2-yl)carbonylamino]-3-(1~{H}-imidazol-4-yl)propanoyl]-~{N}-[(2~{S})-1-azanyl-1-oxidanylidene-propan-2-yl]pyrrolidine-2-carboxamide


Mass: 491.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H29N7O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM Na/K phosphate, 6 % PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9702 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 14, 2009 / Details: none
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9702 Å / Relative weight: 1
ReflectionResolution: 1.35→31.632 Å / Num. obs: 48841 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.662 % / Biso Wilson estimate: 19.304 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.087 / Χ2: 1.098 / Net I/σ(I): 13.75 / Num. measured all: 325400
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.35-1.435.8840.6362.1744571781775750.7690.69896.9
1.43-1.537.140.44.1552534735873580.930.432100
1.53-1.657.1370.2537.0949029687068700.9670.273100
1.65-1.817.0920.17110.9744968634163410.9850.184100
1.81-2.036.850.1116.7939629578557850.9930.119100
2.03-2.346.5240.07822.6233225509350930.9950.084100
2.34-2.866.3560.06426.7727898438943890.9970.069100
2.86-4.036.1570.05331.6721113342934290.9980.057100
4.03-31.6326.2130.04133.8812433202120010.9980.04599

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.23data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B32

4b32


Resolution: 1.352→31.632 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 19.9
RfactorNum. reflection% reflection
Rfree0.21 2466 5.05 %
Rwork0.1869 --
obs0.1881 48835 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.5 Å2 / Biso mean: 18.1833 Å2 / Biso min: 4.11 Å2
Refinement stepCycle: final / Resolution: 1.352→31.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 75 358 2202
Biso mean--26.43 28.96 -
Num. residues----227
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.352-1.3780.28951300.2637233292
1.378-1.40620.24761560.24352520100
1.4062-1.43670.26431340.22252556100
1.4367-1.47020.21711190.2172570100
1.4702-1.50690.2441480.20962537100
1.5069-1.54770.24151270.20242575100
1.5477-1.59320.21591190.19862574100
1.5932-1.64460.21981370.19952567100
1.6446-1.70340.21961250.1942575100
1.7034-1.77160.24041340.19082576100
1.7716-1.85220.23311330.1912593100
1.8522-1.94990.20761340.18982583100
1.9499-2.0720.2191280.17752591100
2.072-2.23190.19361620.17792560100
2.2319-2.45650.1911390.17992610100
2.4565-2.81170.22621370.18842634100
2.8117-3.54170.19941600.17572638100
3.5417-31.6320.18371440.1706277899

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