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- PDB-5j4h: Structure of humanised RadA-mutant humRadA22F in complex with ind... -

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Basic information

Entry
Database: PDB / ID: 5j4h
TitleStructure of humanised RadA-mutant humRadA22F in complex with indole-6-carboxylic acid
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
1H-indole-6-carboxylic acid / DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.374 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 1.2May 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 / 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)25,7246
Polymers25,3991
Non-polymers3255
Water4,972276
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-25 kcal/mol
Surface area10970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.459, 61.122, 87.767
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, 281 molecules

#2: Chemical ChemComp-1F1 / 1H-indole-6-carboxylic acid


Mass: 161.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7NO2
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 42.42 % / 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% PEG 8000, 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: 1.374→61.122 Å / Num. obs: 44591 / % possible obs: 96.5 % / Redundancy: 5.3 % / Biso Wilson estimate: 12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rsym value: 0.062 / Net I/σ(I): 17.7
Reflection shellResolution: 1.374→1.378 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2 / % possible all: 76.7

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Processing

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

Resolution: 1.374→50.157 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.9 / Phase error: 14.91
RfactorNum. reflection% reflection
Rfree0.1698 2241 5.03 %
Rwork0.1324 --
obs0.1342 44537 96.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.374→50.157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1747 0 19 276 2042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041934
X-RAY DIFFRACTIONf_angle_d0.8652628
X-RAY DIFFRACTIONf_dihedral_angle_d12.496754
X-RAY DIFFRACTIONf_chiral_restr0.051293
X-RAY DIFFRACTIONf_plane_restr0.003365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3735-1.40340.26461220.2052194X-RAY DIFFRACTION81
1.4034-1.4360.22021460.17542437X-RAY DIFFRACTION91
1.436-1.47190.24551380.15752528X-RAY DIFFRACTION94
1.4719-1.51170.19321550.14352623X-RAY DIFFRACTION96
1.5117-1.55620.18661140.12962619X-RAY DIFFRACTION96
1.5562-1.60650.17961410.11922641X-RAY DIFFRACTION98
1.6065-1.66390.1861390.11792642X-RAY DIFFRACTION98
1.6639-1.73050.17581630.11752639X-RAY DIFFRACTION98
1.7305-1.80930.14361460.11542648X-RAY DIFFRACTION98
1.8093-1.90470.16021620.11692658X-RAY DIFFRACTION98
1.9047-2.0240.16431300.11332710X-RAY DIFFRACTION98
2.024-2.18030.14341270.11212716X-RAY DIFFRACTION99
2.1803-2.39970.13181410.112721X-RAY DIFFRACTION99
2.3997-2.74690.15331330.12462780X-RAY DIFFRACTION99
2.7469-3.46070.19491380.1372810X-RAY DIFFRACTION100
3.4607-50.19090.16481460.15712930X-RAY DIFFRACTION99

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