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- PDB-7omw: Thermus sp. 2.9 DarT in complex with NAD+ -

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Basic information

Entry
Database: PDB / ID: 7omw
TitleThermus sp. 2.9 DarT in complex with NAD+
ComponentsDarT 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / THIOCYANATE ION / DNA ADP-ribosyl transferase
Similarity search - Component
Biological speciesThermus sp. 2.9 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._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
Revision 1.2May 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4356
Polymers24,4371
Non-polymers9985
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-15 kcal/mol
Surface area9820 Å2
Unit cell
Length a, b, c (Å)36.032, 61.745, 50.197
Angle α, β, γ (deg.)90.000, 95.198, 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: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 50 mM potassium thiocyanate, 20% (w/v) PEG2000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→35.909 Å / Num. obs: 52232 / % possible obs: 97 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.017 / Rrim(I) all: 0.045 / Net I/σ(I): 20.3
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1891 / CC1/2: 0.949 / Rpim(I) all: 0.155 / Rrim(I) all: 0.277

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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: 1.3→35.909 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.509 / SU ML: 0.028 / Cross valid method: FREE R-VALUE / ESU R: 0.042 / ESU R Free: 0.04
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1525 2518 4.823 %
Rwork0.131 49690 -
all0.132 --
obs-52208 96.899 %
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: 17.786 Å2
Baniso -1Baniso -2Baniso -3
1-1.524 Å20 Å2-2.648 Å2
2---0.37 Å2-0 Å2
3----0.662 Å2
Refinement stepCycle: LAST / Resolution: 1.3→35.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1627 0 65 175 1867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131792
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171672
X-RAY DIFFRACTIONr_angle_refined_deg1.8031.6582447
X-RAY DIFFRACTIONr_angle_other_deg1.451.5743865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.765211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.89420.60699
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32615285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg191515
X-RAY DIFFRACTIONr_chiral_restr0.1050.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021993
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02433
X-RAY DIFFRACTIONr_nbd_refined0.2730.2331
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.21592
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2825
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2813
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2104
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0240.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3530.215
X-RAY DIFFRACTIONr_nbd_other0.2210.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2720.217
X-RAY DIFFRACTIONr_mcbond_it1.8171.448807
X-RAY DIFFRACTIONr_mcbond_other1.8161.446805
X-RAY DIFFRACTIONr_mcangle_it2.2212.1781008
X-RAY DIFFRACTIONr_mcangle_other2.222.1771009
X-RAY DIFFRACTIONr_scbond_it3.0831.942985
X-RAY DIFFRACTIONr_scbond_other3.0391.943985
X-RAY DIFFRACTIONr_scangle_it3.8272.741431
X-RAY DIFFRACTIONr_scangle_other3.8112.7411431
X-RAY DIFFRACTIONr_lrange_it4.17618.2821993
X-RAY DIFFRACTIONr_lrange_other3.81717.9711970
X-RAY DIFFRACTIONr_rigid_bond_restr7.61733464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.3340.181600.182747X-RAY DIFFRACTION73.0035
1.334-1.370.1761680.1763202X-RAY DIFFRACTION86.9453
1.37-1.410.1671860.1483468X-RAY DIFFRACTION98.2786
1.41-1.4530.151980.1413468X-RAY DIFFRACTION100
1.453-1.5010.1621490.1243416X-RAY DIFFRACTION100
1.501-1.5540.151460.1093280X-RAY DIFFRACTION99.9708
1.554-1.6120.1181420.1033139X-RAY DIFFRACTION100
1.612-1.6780.1271620.0993016X-RAY DIFFRACTION100
1.678-1.7530.1271570.0982899X-RAY DIFFRACTION100
1.753-1.8380.1391200.12799X-RAY DIFFRACTION100
1.838-1.9370.1341370.1032664X-RAY DIFFRACTION100
1.937-2.0550.1211100.1112499X-RAY DIFFRACTION100
2.055-2.1960.1411100.1162368X-RAY DIFFRACTION99.9597
2.196-2.3720.1181110.1162226X-RAY DIFFRACTION100
2.372-2.5980.1461220.1181990X-RAY DIFFRACTION100
2.598-2.9040.143940.1321828X-RAY DIFFRACTION100
2.904-3.3520.146860.1441628X-RAY DIFFRACTION100
3.352-4.1030.175690.1491371X-RAY DIFFRACTION100
4.103-5.7890.188550.1541076X-RAY DIFFRACTION100
5.789-35.9090.26360.214606X-RAY DIFFRACTION99.6894

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