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- PDB-5jee: Apo-structure of humanised RadA-mutant humRadA26F -

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Basic information

Entry
Database: PDB / ID: 5jee
TitleApo-structure of humanised RadA-mutant humRadA26F
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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: 1.49 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.
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 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Feb 7, 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)25,4132
Polymers25,3731
Non-polymers401
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-12 kcal/mol
Surface area10850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.581, 50.597, 74.269
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: 25372.965 Da / Num. of mol.: 1
Mutation: S167K, V168A, I169M, W170Y, I182L, R183L, K198D, H199N, I200V, Y201A, V202Y, E219S, K221M, I222M
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 1.87 Å3/Da / Density % sol: 34.32 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1M NaAcetate pH=4.6, 15% PEG20K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.487→74.269 Å / Num. obs: 31823 / % possible obs: 99.3 % / Redundancy: 6.6 % / Biso Wilson estimate: 22.53 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.068 / Net I/σ(I): 17.5
Reflection shellResolution: 1.487→1.492 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 2.2 / % possible all: 87.6

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5j4l

5j4l


Resolution: 1.49→37.13 Å / Cor.coef. Fo:Fc: 0.9502 / Cor.coef. Fo:Fc free: 0.942 / SU R Cruickshank DPI: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.08 / SU Rfree Blow DPI: 0.079 / SU Rfree Cruickshank DPI: 0.078
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 1617 5.12 %RANDOM
Rwork0.1939 ---
obs0.1951 31579 99.25 %-
Displacement parametersBiso mean: 33.49 Å2
Baniso -1Baniso -2Baniso -3
1-6.9676 Å20 Å20 Å2
2---8.8944 Å20 Å2
3---1.9268 Å2
Refinement stepCycle: 1 / Resolution: 1.49→37.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 1 87 1834
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011774HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.262397HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d653SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes49HARMONIC2
X-RAY DIFFRACTIONt_gen_planes263HARMONIC5
X-RAY DIFFRACTIONt_it1774HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.96
X-RAY DIFFRACTIONt_other_torsion17.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion232SEMIHARMONIC5
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_contact2130SEMIHARMONIC4
LS refinement shellResolution: 1.49→1.54 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2321 146 5.46 %
Rwork0.232 2529 -
all0.232 2675 -
obs--99.25 %

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