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- PDB-5lb2: Apo-structure of humanised RadA-mutant humRadA2 -

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Basic information

Entry
Database: PDB / ID: 5lb2
TitleApo-structure of humanised RadA-mutant humRadA2
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: 2.1 Å
AuthorsMarsh, M. / Fischer, G. / Moschetti, T. / Sharpe, T. / Scott, D. / Morgan, M. / Ng, H. / Skidmore, J. / Venkitaraman, A. / Abell, C. ...Marsh, M. / Fischer, G. / 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
DepositionJun 15, 2016Deposition site: PDBE / 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


Theoretical massNumber of molelcules
Total (without water)25,3021
Polymers25,3021
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.040, 90.040, 67.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-435-

HOH

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Components

#1: Protein DNA repair and recombination protein RadA


Mass: 25302.002 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 (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O74036
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.12 Å3/Da / Density % sol: 60.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 25% PEG6000, 100 mM MES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 18731 / % possible obs: 99.7 % / Redundancy: 10.9 % / Biso Wilson estimate: 44.36 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.051 / Net I/σ(I): 29.46
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 4.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A6P

4a6p


Resolution: 2.1→45.02 Å / Cor.coef. Fo:Fc: 0.9409 / Cor.coef. Fo:Fc free: 0.9262 / SU R Cruickshank DPI: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.178 / SU Rfree Blow DPI: 0.16 / SU Rfree Cruickshank DPI: 0.163
RfactorNum. reflection% reflectionSelection details
Rfree0.2524 964 5.15 %RANDOM
Rwork0.2217 ---
obs0.2232 18731 99.12 %-
Displacement parametersBiso mean: 50.05 Å2
Baniso -1Baniso -2Baniso -3
1--1.1016 Å20 Å20 Å2
2---1.1016 Å20 Å2
3---2.2032 Å2
Refine analyzeLuzzati coordinate error obs: 0.326 Å
Refinement stepCycle: 1 / Resolution: 2.1→45.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 0 41 1759
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011744HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.112352HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d630SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes45HARMONIC2
X-RAY DIFFRACTIONt_gen_planes254HARMONIC5
X-RAY DIFFRACTIONt_it1744HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion19.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion231SEMIHARMONIC5
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_contact1964SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.23 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2761 156 5.42 %
Rwork0.2657 2720 -
all0.2663 2876 -
obs--95.77 %

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