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- PDB-7on0: Thermus sp. 2.9 DarT in complex with ADP-ribosylated ssDNA -

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Basic information

Entry
Database: PDB / ID: 7on0
TitleThermus sp. 2.9 DarT in complex with ADP-ribosylated ssDNA
Components
  • DNA (5'-D(*AP*TP*GP*TP*C)-3')
  • DarT domain-containing protein
KeywordsTOXIN / TOXIN-ANTITOXIN / DNA ADP-RIBOSYLATION / ADP-ribosyltransferase activity / DNA binding
Function / homology
Function and homology information


glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / DNA binding
Similarity search - Function
DNA ADP-ribosyl transferase (DarT) domain profile. / ssDNA thymidine ADP-ribosyltransferase, DarT / ssDNA thymidine ADP-ribosyltransferase, DarT
Similarity search - Domain/homology
Chem-AR6 / DNA / DNA ADP-ribosyl transferase
Similarity search - Component
Biological speciesThermus sp. 2.9 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsSchuller, M. / Ariza, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R007195/1 United Kingdom
CitationJournal: Nature / Year: 2021
Title: Molecular basis for DarT ADP-ribosylation of a DNA base.
Authors: Schuller, M. / Butler, R.E. / Ariza, A. / Tromans-Coia, C. / Jankevicius, G. / Claridge, T.D.W. / Kendall, S.L. / Goh, S. / Stewart, G.R. / Ahel, I.
History
DepositionMay 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 2.0Oct 13, 2021Group: Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / citation / citation_author / database_2 / diffrn_source / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _atom_site.pdbx_tls_group_id / _citation.country ..._atom_site.pdbx_tls_group_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 2.1May 1, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: DarT domain-containing protein
AaA: DNA (5'-D(*AP*TP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4923
Polymers25,9322
Non-polymers5591
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-10 kcal/mol
Surface area10270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.889, 38.683, 61.012
Angle α, β, γ (deg.)90.000, 101.756, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DarT domain-containing protein


Mass: 24437.170 Da / Num. of mol.: 1 / Mutation: E160A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus sp. 2.9 (bacteria) / Gene: QT17_01930 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A0B0SG80
#2: DNA chain DNA (5'-D(*AP*TP*GP*TP*C)-3')


Mass: 1495.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus sp. 2.9 (bacteria)
#3: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 1.87 Å3/Da / Density % sol: 34.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 123 mM potassium thiocyanate, 12% (w/v) PEG2000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.8998 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8998 Å / Relative weight: 1
ReflectionResolution: 1.46→38.68 Å / Num. obs: 33508 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.057 / Rrim(I) all: 0.144 / Net I/σ(I): 7.4
Reflection shellResolution: 1.46→1.49 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.307 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1649 / CC1/2: 0.513 / Rpim(I) all: 0.623 / Rrim(I) all: 1.452 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292116023

Resolution: 1.46→32.49 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.203 / SU ML: 0.058 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1903 1622 4.843 %
Rwork0.1622 31869 -
all0.164 --
obs-33491 99.958 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.031 Å2
Baniso -1Baniso -2Baniso -3
1--0.394 Å20 Å2-0.398 Å2
2--0.377 Å20 Å2
3---0.169 Å2
Refinement stepCycle: LAST / Resolution: 1.46→32.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1724 98 35 226 2083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0121939
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171763
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.6292663
X-RAY DIFFRACTIONr_angle_other_deg1.4771.6214066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0265212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.30520.481104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03815296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1051516
X-RAY DIFFRACTIONr_chiral_restr0.0950.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022094
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02469
X-RAY DIFFRACTIONr_nbd_refined0.2410.2367
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.21744
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2904
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2927
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2147
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3240.214
X-RAY DIFFRACTIONr_nbd_other0.2410.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2420.227
X-RAY DIFFRACTIONr_mcbond_it0.9131.114839
X-RAY DIFFRACTIONr_mcbond_other0.9121.114838
X-RAY DIFFRACTIONr_mcangle_it1.3741.6681048
X-RAY DIFFRACTIONr_mcangle_other1.3741.6681049
X-RAY DIFFRACTIONr_scbond_it1.5921.3291100
X-RAY DIFFRACTIONr_scbond_other1.5911.3291101
X-RAY DIFFRACTIONr_scangle_it2.3971.9191613
X-RAY DIFFRACTIONr_scangle_other2.3961.9191614
X-RAY DIFFRACTIONr_lrange_it4.48414.0982252
X-RAY DIFFRACTIONr_lrange_other4.35313.5472210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.4980.2761100.2822360X-RAY DIFFRACTION99.9191
1.498-1.5390.2541170.2592294X-RAY DIFFRACTION100
1.539-1.5840.2441120.2322195X-RAY DIFFRACTION100
1.584-1.6320.2571070.2162148X-RAY DIFFRACTION100
1.632-1.6860.2491040.1962100X-RAY DIFFRACTION100
1.686-1.7450.221040.182036X-RAY DIFFRACTION100
1.745-1.8110.24990.1761926X-RAY DIFFRACTION99.9013
1.811-1.8840.1911030.1691874X-RAY DIFFRACTION100
1.884-1.9680.192860.1621841X-RAY DIFFRACTION100
1.968-2.0640.204960.1611686X-RAY DIFFRACTION100
2.064-2.1760.174800.1521657X-RAY DIFFRACTION100
2.176-2.3070.175710.1471575X-RAY DIFFRACTION100
2.307-2.4670.178850.151461X-RAY DIFFRACTION100
2.467-2.6640.186800.1431349X-RAY DIFFRACTION100
2.664-2.9170.199610.1471269X-RAY DIFFRACTION100
2.917-3.2610.217630.1421142X-RAY DIFFRACTION100
3.261-3.7630.153460.1381019X-RAY DIFFRACTION100
3.763-4.6050.142420.121864X-RAY DIFFRACTION100
4.605-6.4930.13380.162675X-RAY DIFFRACTION99.8599
6.493-32.490.19180.176398X-RAY DIFFRACTION99.284
Refinement TLS params.Method: refined / Origin x: 6.383 Å / Origin y: 1.245 Å / Origin z: 15.1831 Å
111213212223313233
T0.0085 Å20.0006 Å20.0028 Å2-0.0242 Å2-0.0065 Å2--0.0335 Å2
L0.6952 °20.0149 °20.4662 °2-0.1881 °20.0224 °2--0.3326 °2
S-0.0345 Å °-0.0959 Å °-0.0359 Å °-0.0292 Å °0.0399 Å °-0.0428 Å °-0.0312 Å °-0.0644 Å °-0.0054 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA1 - 209
2X-RAY DIFFRACTION1ALLAaA301 - 305

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