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- PDB-5j4k: Structure of humanised RadA-mutant humRadA22F in complex with 1-I... -

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Basic information

Entry
Database: PDB / ID: 5j4k
TitleStructure of humanised RadA-mutant humRadA22F in complex with 1-Indane-6-carboxylic acid
ComponentsDNA repair and recombination protein RadA
KeywordsHYDROLASE / DNA repair / fragment based drug design / humanisation
Function / homology
Function and homology information


DNA recombinase assembly / mitotic recombination / DNA strand invasion / DNA strand exchange activity / ATP-dependent DNA damage sensor activity / single-stranded DNA binding / double-stranded DNA binding / damaged DNA binding / 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
2,3-dihydro-1H-indene-2-carboxylic acid / DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.346 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 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)25,7396
Polymers25,3991
Non-polymers3405
Water4,342241
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-26 kcal/mol
Surface area11020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.440, 61.214, 87.742
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 246 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-6FZ / 2,3-dihydro-1H-indene-2-carboxylic acid


Mass: 162.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.19 Å3/Da / Density % sol: 43.73 %
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 soaking: 10% DMSO, 5mM compound

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.346→50.204 Å / Num. obs: 46330 / % possible obs: 94.4 % / Redundancy: 6.3 % / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 24.9
Reflection shellResolution: 1.346→1.35 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 2.1 / % possible all: 58.5

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Processing

Software
NameVersionClassification
autoPROCdata reduction
SCALAdata scaling
PHENIX1.9_1692refinement
PHASERphasing
Cootmodel building
BUSTERrefinement
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo_structure

Resolution: 1.346→50.204 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 14.15
RfactorNum. reflection% reflection
Rfree0.1638 2322 5.02 %
Rwork0.1285 --
obs0.1302 46275 94.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.346→50.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1747 0 21 241 2009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081892
X-RAY DIFFRACTIONf_angle_d1.1192565
X-RAY DIFFRACTIONf_dihedral_angle_d13.071733
X-RAY DIFFRACTIONf_chiral_restr0.066289
X-RAY DIFFRACTIONf_plane_restr0.005348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3456-1.37310.2726810.20761731X-RAY DIFFRACTION64
1.3731-1.40290.22961160.19242153X-RAY DIFFRACTION80
1.4029-1.43560.21141520.16382476X-RAY DIFFRACTION93
1.4356-1.47150.20721380.14292582X-RAY DIFFRACTION95
1.4715-1.51130.18341590.12742604X-RAY DIFFRACTION96
1.5113-1.55570.16171140.11372624X-RAY DIFFRACTION96
1.5557-1.60590.15681380.1052604X-RAY DIFFRACTION97
1.6059-1.66340.18071410.10592642X-RAY DIFFRACTION97
1.6634-1.730.15081580.10522632X-RAY DIFFRACTION97
1.73-1.80870.1451480.10842650X-RAY DIFFRACTION97
1.8087-1.9040.15611620.10682643X-RAY DIFFRACTION97
1.904-2.02330.17341280.1072699X-RAY DIFFRACTION97
2.0233-2.17960.13391290.10642701X-RAY DIFFRACTION99
2.1796-2.39890.11871350.10822717X-RAY DIFFRACTION98
2.3989-2.7460.15851380.12152769X-RAY DIFFRACTION99
2.746-3.45960.18231390.13552799X-RAY DIFFRACTION99
3.4596-50.23860.16831460.15972927X-RAY DIFFRACTION99

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