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- PDB-6xtw: HumRadA33F in complex with peptidic inhibitor 6 -

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Basic information

Entry
Database: PDB / ID: 6xtw
TitleHumRadA33F in complex with peptidic inhibitor 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: 2.31 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 16, 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
B: DNA repair and recombination protein RadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1325
Polymers50,4802
Non-polymers6533
Water2,126118
1
A: DNA repair and recombination protein RadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7963
Polymers25,2401
Non-polymers5572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA repair and recombination protein RadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3362
Polymers25,2401
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.831, 89.831, 100.825
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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Components

#1: Protein DNA repair and recombination protein RadA


Mass: 25239.799 Da / Num. of mol.: 2 / 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
Details: Humanised RadA HumRadA22F
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5 / Details: 22% PEG3350, 0.1 M BisTris pH5.0, 0.2 M LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.93 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2012 / Details: none
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.31→100.825 Å / Num. obs: 21180 / % possible obs: 99.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.036 / Rrim(I) all: 0.082 / Net I/σ(I): 14.4
Reflection shellResolution: 2.31→2.43 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 16048 / Rpim(I) all: 0.435 / Rrim(I) all: 0.767 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
SCALAdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JEC

5jec


Resolution: 2.31→44.92 Å / SU ML: 0.2796 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.5471
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 1036 4.94 %RANDOM
Rwork0.1841 19921 --
obs0.1863 20957 99.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.93 Å2
Refinement stepCycle: LAST / Resolution: 2.31→44.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3494 0 44 118 3656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00683597
X-RAY DIFFRACTIONf_angle_d0.86234851
X-RAY DIFFRACTIONf_chiral_restr0.0542549
X-RAY DIFFRACTIONf_plane_restr0.0054650
X-RAY DIFFRACTIONf_dihedral_angle_d23.13482182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.430.28161380.24992826X-RAY DIFFRACTION99.76
2.43-2.580.29771610.22912790X-RAY DIFFRACTION99.76
2.58-2.780.22741510.22152824X-RAY DIFFRACTION99.63
2.78-3.060.27341640.20932822X-RAY DIFFRACTION99.33
3.06-3.510.25531450.19342799X-RAY DIFFRACTION98.66
3.51-4.420.23451400.16262877X-RAY DIFFRACTION99.31
4.42-44.920.1731370.16292983X-RAY DIFFRACTION98.61

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