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- PDB-6tuu: Leishmania infantum Rad51 surrogate LiRadA10 in complex with 5,6,... -

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Basic information

Entry
Database: PDB / ID: 6tuu
TitleLeishmania infantum Rad51 surrogate LiRadA10 in complex with 5,6,7,8-tetrahydro-2-naphthoic acid
ComponentsDNA repair and recombination protein RadA
KeywordsRECOMBINATION / Recombinase / FBDD / Fragment / Surrogate / RadA / Rad51 / Archaeal
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
5,6,7,8-tetrahydronaphthalene-2-carboxylic acid / PHOSPHATE ION / DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsPantelejevs, T. / Hyvonen, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: Development of dedicated crystallographic systems for structure-guided drug discovery
Authors: Brear, P. / Pantelejevs, T. / Hyvonen, M.
History
DepositionJan 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: DNA repair and recombination protein RadA
B: DNA repair and recombination protein RadA
C: DNA repair and recombination protein RadA
D: DNA repair and recombination protein RadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,29911
Polymers106,3694
Non-polymers9307
Water10,809600
1
A: DNA repair and recombination protein RadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8633
Polymers26,5921
Non-polymers2712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA repair and recombination protein RadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8633
Polymers26,5921
Non-polymers2712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA repair and recombination protein RadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8043
Polymers26,5921
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA repair and recombination protein RadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7682
Polymers26,5921
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.271, 118.976, 83.790
Angle α, β, γ (deg.)90.000, 91.420, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA repair and recombination protein RadA


Mass: 26592.275 Da / Num. of mol.: 4
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O74036
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-NY5 / 5,6,7,8-tetrahydronaphthalene-2-carboxylic acid


Mass: 176.212 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 1.98 Å3/Da / Density % sol: 38.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 20 %w/v PEG 1K (Precipitant), 0.1 M Na K Phos 6.2 pH (Buffer), 0.2 M NaCl (Salt)

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 1.735→48.5 Å / Num. obs: 80648 / % possible obs: 99.1 % / Redundancy: 4 % / Biso Wilson estimate: 28.88 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 8.2
Reflection shellResolution: 1.735→1.765 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.866 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 259450 / Rsym value: 0.866 / % possible all: 98.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5jfg

5jfg


Resolution: 1.74→41.88 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.134 / SU Rfree Blow DPI: 0.123 / SU Rfree Cruickshank DPI: 0.122
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3999 4.96 %RANDOM
Rwork0.196 ---
obs0.198 80642 99.1 %-
Displacement parametersBiso max: 187.76 Å2 / Biso mean: 33.51 Å2 / Biso min: 13.59 Å2
Baniso -1Baniso -2Baniso -3
1-5.377 Å20 Å2-0.029 Å2
2---6.2341 Å20 Å2
3---0.8571 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.74→41.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6779 0 107 600 7486
Biso mean--40.12 47.87 -
Num. residues----884
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2539SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1266HARMONIC5
X-RAY DIFFRACTIONt_it7052HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion919SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8709SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7052HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9567HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion16.43
LS refinement shellResolution: 1.74→1.75 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.1953 78 4.84 %
Rwork0.2056 1535 -
all0.2051 1613 -
obs--99.16 %

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