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- PDB-5j4l: Apo-structure of humanised RadA-mutant humRadA22F -

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Basic information

Entry
Database: PDB / ID: 5j4l
TitleApo-structure of humanised RadA-mutant humRadA22F
ComponentsDNA repair and recombination protein RadA
KeywordsHYDROLASE / DNA repair / fragment based drug design / humanisation
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 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsFischer, G. / Marsh, M. / Moschetti, T. / Sharpe, T. / Scott, D. / Morgan, M. / Ng, H. / Skidmore, J. / Venkitaraman, A. / Abell, C. ...Fischer, G. / Marsh, M. / Moschetti, T. / Sharpe, T. / Scott, D. / Morgan, M. / Ng, H. / Skidmore, J. / Venkitaraman, A. / Abell, C. / Blundell, T.L. / Hyvonen, M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust080083/Z/06/Z United Kingdom
Wellcome Trust91050/Z/10/Z United Kingdom
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Engineering Archeal Surrogate Systems for the Development of Protein-Protein Interaction Inhibitors against Human RAD51.
Authors: Moschetti, T. / Sharpe, T. / Fischer, G. / Marsh, M.E. / Ng, H.K. / Morgan, M. / Scott, D.E. / Blundell, T.L. / R Venkitaraman, A. / Skidmore, J. / Abell, C. / Hyvonen, M.
History
DepositionApr 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 29, 2023Group: Database references / Category: database_2
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)25,4342
Polymers25,3991
Non-polymers351
Water5,368298
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-12 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.481, 61.060, 87.911
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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
Mutation: V168A, I169M, W170Y, I182L, K198D, H199N, I200V, Y201A, V202Y, K221M
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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.49 % / Description: elongated plates
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.08M NaCacodylate, pH=6.5, 0.16M CaAcetate, 18% PEG8000, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.13→30 Å / Num. obs: 148188 / % possible obs: 93.7 % / Redundancy: 3.06 % / Biso Wilson estimate: 9.2 Å2 / CC1/2: 0.999 / Rsym value: 0.051 / Net I/σ(I): 14.8
Reflection shellResolution: 1.13→1.2 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.03 / % possible all: 67.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→26.764 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 12.8
RfactorNum. reflection% reflection
Rfree0.1447 3954 5.01 %
Rwork0.1234 --
obs0.1245 78955 95.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.13→26.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 1 298 2055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091978
X-RAY DIFFRACTIONf_angle_d1.132690
X-RAY DIFFRACTIONf_dihedral_angle_d29.826774
X-RAY DIFFRACTIONf_chiral_restr0.2300
X-RAY DIFFRACTIONf_plane_restr0.006362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.14380.23011020.22411758X-RAY DIFFRACTION65
1.1438-1.15830.2214940.1941940X-RAY DIFFRACTION70
1.1583-1.17350.19311150.18352204X-RAY DIFFRACTION80
1.1735-1.18960.19121200.17332426X-RAY DIFFRACTION87
1.1896-1.20660.18351370.16112532X-RAY DIFFRACTION93
1.2066-1.22460.18511500.15012673X-RAY DIFFRACTION96
1.2246-1.24380.17671460.13962720X-RAY DIFFRACTION99
1.2438-1.26410.15031550.13412734X-RAY DIFFRACTION99
1.2641-1.28590.15741380.12682754X-RAY DIFFRACTION100
1.2859-1.30930.16771220.12052785X-RAY DIFFRACTION100
1.3093-1.33450.13491420.11972735X-RAY DIFFRACTION100
1.3345-1.36170.14681470.11692778X-RAY DIFFRACTION100
1.3617-1.39140.13861450.11462774X-RAY DIFFRACTION100
1.3914-1.42370.17491430.10972756X-RAY DIFFRACTION100
1.4237-1.45930.12951550.1062771X-RAY DIFFRACTION100
1.4593-1.49880.13281450.10182773X-RAY DIFFRACTION100
1.4988-1.54290.12071520.0942758X-RAY DIFFRACTION100
1.5429-1.59270.12471310.09412806X-RAY DIFFRACTION100
1.5927-1.64960.11111340.0982783X-RAY DIFFRACTION100
1.6496-1.71560.12241450.10552791X-RAY DIFFRACTION100
1.7156-1.79370.1471620.10832793X-RAY DIFFRACTION100
1.7937-1.88820.12161460.11372791X-RAY DIFFRACTION100
1.8882-2.00650.12621100.11122855X-RAY DIFFRACTION100
2.0065-2.16140.14731610.11232804X-RAY DIFFRACTION100
2.1614-2.37870.13691830.11422800X-RAY DIFFRACTION100
2.3787-2.72270.14191600.12312832X-RAY DIFFRACTION100
2.7227-3.42910.14291500.12882869X-RAY DIFFRACTION100
3.4291-26.77160.15131640.14313006X-RAY DIFFRACTION100

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