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- PDB-6xuf: HumRadA1 in complex with 5-Ethyl-N-(1H-indol-5-ylmethyl)-1,3,4-th... -

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Basic information

Entry
Database: PDB / ID: 6xuf
TitleHumRadA1 in complex with 5-Ethyl-N-(1H-indol-5-ylmethyl)-1,3,4-thiadiazol-2-amine in P21
ComponentsDNA repair and recombination protein RadA
KeywordsRECOMBINATION / recombinase / ATPase / protein-fragment complex / protein engineering
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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-O1E / PHOSPHATE ION / DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.241 Å
AuthorsMarsh, M.E. / Scott, D.E. / Hyvonen, M.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust080083/Z/06/Z United Kingdom
CitationJournal: To be published
Title: Optimising crystallographic systems for structure-guided drug discovery
Authors: Brear, P.D. / Marsh, M. / Fischer, G. / Hyvonen, M.
History
DepositionJan 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: DNA repair and recombination protein RadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8553
Polymers25,5021
Non-polymers3532
Water5,495305
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-7 kcal/mol
Surface area10400 Å2
Unit cell
Length a, b, c (Å)37.630, 78.960, 39.520
Angle α, β, γ (deg.)90.000, 117.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA repair and recombination protein RadA


Mass: 25502.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: O74036
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-O1E / 5-Ethyl-N-(1H-indol-5-ylmethyl)-1,3,4-thiadiazol-2-amine / 5-ethyl-~{N}-(1~{H}-indol-5-ylmethyl)-1,3,4-thiadiazol-2-amine


Mass: 258.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14N4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 50 mM Na/K PHOSPHATE, 5% PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97957 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 10, 2008 / Details: none
RadiationMonochromator: none / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.24→31.963 Å / Num. obs: 56612 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.534 % / Biso Wilson estimate: 18.401 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.053 / Χ2: 0.986 / Net I/σ(I): 14.88 / Num. measured all: 200049
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.24-1.322.7750.4842.0623599931685040.7930.58991.3
1.32-1.413.6230.3413.6431479874486890.9110.40199.4
1.41-1.523.6570.1926.4129723816681270.9660.22599.5
1.52-1.663.6810.10810.9227467748874620.9880.12799.7
1.66-1.863.6970.06616.7924934677267440.9950.07899.6
1.86-2.153.7130.04325.4722214602159830.9970.0599.4
2.15-2.633.6860.03632.418662509650630.9980.04299.4
2.63-3.73.6660.03137.2514409396239300.9980.03799.2
3.7-31.9633.5840.0339.677562223721100.9980.03594.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.23data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4b3b

4b3b


Resolution: 1.241→31.963 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18
RfactorNum. reflection% reflection
Rfree0.1863 2897 5.12 %
Rwork0.1578 --
obs0.1593 56605 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.54 Å2 / Biso mean: 20.5407 Å2 / Biso min: 4.82 Å2
Refinement stepCycle: final / Resolution: 1.241→31.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 37 305 2056
Biso mean--22.5 35.54 -
Num. residues----220
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.241-1.2610.26661140.2728197576
1.261-1.28280.24271260.2358249696
1.2828-1.30610.26651260.2089256999
1.3061-1.33120.2231270.1857259699
1.3312-1.35840.20551750.17822577100
1.3584-1.38790.20731280.1732258899
1.3879-1.42020.21631240.16532597100
1.4202-1.45570.20971360.16462577100
1.4557-1.49510.17081440.1522583100
1.4951-1.53910.19561520.13842584100
1.5391-1.58880.18851530.13062605100
1.5888-1.64560.15261450.13462590100
1.6456-1.71140.18151320.142603100
1.7114-1.78930.19271450.14622588100
1.7893-1.88360.18721420.14392616100
1.8836-2.00160.15981300.14712588100
2.0016-2.15620.16891570.14492568100
2.1562-2.37310.17411330.15142622100
2.3731-2.71630.16731330.16262615100
2.7163-3.42160.19181390.16362617100
3.4216-31.9630.19241360.1598255496

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