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- PDB-6xuj: 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: 6xuj
TitleHumRadA1 in complex with 5-Ethyl-N-(1H-indol-5-ylmethyl)-1,3,4-thiadiazol-2-amine in P21212
ComponentsDNA repair and recombination protein RadA
KeywordsRECOMBINATION / recombinase / ATPase / protein-fragment complex
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: 1.54 Å
AuthorsMarsh, M.E. / Scott, D.E. / Hyvonen, M.
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.B. / Marsh, M. / Hyvonen, M.
History
DepositionJan 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 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
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-8 kcal/mol
Surface area10390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.453, 73.211, 40.793
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-719-

HOH

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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 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-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.03 Å3/Da / Density % sol: 39.51 %
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: I03 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2008
RadiationMonochromator: none / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.54→40.793 Å / Num. obs: 31313 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 4.929 % / Biso Wilson estimate: 21.363 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.082 / Χ2: 0.937 / Net I/σ(I): 13.77 / Num. measured all: 154352
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
1.54-1.633.9440.4552.8518757505747560.8540.52494
1.63-1.745.120.2985.1924295474947450.9490.33399.9
1.74-1.885.1420.1718.5622677441844100.9790.19199.8
1.88-2.065.1650.113.6421178411141000.9910.11299.7
2.06-2.35.1590.07118.1919048370036920.9950.0899.8
2.3-2.665.1560.06221.3817021330833010.9940.0799.8
2.66-3.255.1040.05623.8114290281428000.9950.06399.5
3.25-4.595.0070.05327.411115223622200.9960.05999.3
4.59-40.7934.6320.05326.415971131912890.9960.0697.7

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Processing

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

4b3b


Resolution: 1.54→36.605 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 1598 5.11 %
Rwork0.1663 29677 -
obs0.1683 31275 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.14 Å2 / Biso mean: 19.1575 Å2 / Biso min: 7.35 Å2
Refinement stepCycle: final / Resolution: 1.54→36.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1739 0 37 250 2026
Biso mean--26.21 32.97 -
Num. residues----224
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.54-1.58970.27921300.2285252694
1.5897-1.64650.2731370.19152679100
1.6465-1.71250.22991470.1732680100
1.7125-1.79040.26511480.17862683100
1.7904-1.88480.23151530.15842669100
1.8848-2.00290.19181370.15342690100
2.0029-2.15750.19341540.15222705100
2.1575-2.37460.18371540.15172691100
2.3746-2.71810.22151350.16312749100
2.7181-3.42410.19241400.1637275399
3.4241-36.6050.18521630.1739285298

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