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- PDB-5qur: HumRadA1 soaked with 2 mM indazole in 10% DMSO -

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Basic information

Entry
Database: PDB / ID: 5qur
TitleHumRadA1 soaked with 2 mM indazole in 10% DMSO
ComponentsRadA
KeywordsDNA BINDING PROTEIN / RAD51 / RadA / inhibition / FBDD / PPI
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
1H-indazole / PHOSPHATE ION / DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.247 Å
AuthorsMarsh, M. / Hyvonen, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust080083/Z/06/Z 91050/Z/10/Z United Kingdom
CitationJournal: To be published
Title: Optimisation of crystal forms for structure-guided drug discovery
Authors: Brear, P.B. / Fischer, G. / Rocaboy, R. / Marsh, M. / Rossmann, M. / Pantelejevs, T. / Wagstaff, J. / Blaszczyk, B.K.
History
DepositionJan 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: RadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7153
Polymers25,5021
Non-polymers2132
Water5,062281
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.052, 61.808, 87.033
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RadA /


Mass: 25502.150 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O74036*PLUS
#2: Chemical ChemComp-LZ1 / 1H-indazole / Indazole


Mass: 118.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 50 mM Na/K phospate, 5% PEG1000H

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9535 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9535 Å / Relative weight: 1
ReflectionResolution: 1.25→43.516 Å / Num. obs: 59987 / % possible obs: 98.3 % / Redundancy: 6.634 % / Biso Wilson estimate: 15.138 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.113 / Χ2: 1.008 / Net I/σ(I): 12.96 / Num. measured all: 397956
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
1.25-1.325.2870.8782.7347216971389310.7130.97491.9
1.32-1.416.9910.6754.2864061916791640.8750.73100
1.41-1.537.0220.4096.560038855185500.9460.442100
1.53-1.677.10.2349.8456236792179210.9770.253100
1.67-1.877.1060.13814.3150804714971490.990.149100
1.87-2.166.8020.08720.3443124635463400.9950.09599.8
2.16-2.646.6940.06326.7336301542854230.9970.06899.9
2.64-3.736.4540.04930.8527292425142290.9980.05399.5
3.73-43.5165.6510.03732.1912884248522800.9980.04191.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.247→43.516 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2086 2980 4.97 %
Rwork0.1833 56999 -
obs0.1845 59979 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.02 Å2 / Biso mean: 15.1895 Å2 / Biso min: 4.16 Å2
Refinement stepCycle: final / Resolution: 1.247→43.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1699 0 20 281 2000
Biso mean--35.02 28.12 -
Num. residues----218
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2475-1.26790.43531050.42732066217176
1.2679-1.28980.31951380.26427152853100
1.2898-1.31320.25741500.219127192869100
1.3132-1.33850.23291460.19927262872100
1.3385-1.36580.25681350.193227042839100
1.3658-1.39550.2621340.200827102844100
1.3955-1.4280.24171420.171627662908100
1.428-1.46370.18561210.175627232844100
1.4637-1.50330.20751480.172727462894100
1.5033-1.54750.20611540.162827172871100
1.5475-1.59750.19061300.153627502880100
1.5975-1.65460.22021310.154727342865100
1.6546-1.72080.18471440.164527592903100
1.7208-1.79910.18831550.154927292884100
1.7991-1.8940.21781460.1727602906100
1.894-2.01270.19291030.162827922895100
2.0127-2.1680.1651710.161527412912100
2.168-2.38620.18791730.162627582931100
2.3862-2.73150.19781560.183727942950100
2.7315-3.44110.2191460.188428312977100
3.4411-43.5430.20111520.20392759291193

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