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- PDB-8baq: E. coli C7 DarT1 in complex with NAD+ -

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Basic information

Entry
Database: PDB / ID: 8baq
TitleE. coli C7 DarT1 in complex with NAD+
ComponentsDarT ssDNA thymidine ADP-ribosyltransferase family protein
KeywordsTOXIN / TOXIN-ANTITOXIN / DNA ADP-RIBOSYLATION / ADP-ribosyltransferase activity / DNA binding
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: Mol.Cell / Year: 2023
Title: Molecular basis for the reversible ADP-ribosylation of guanosine bases.
Authors: Schuller, M. / Raggiaschi, R. / Mikolcevic, P. / Rack, J.G.M. / Ariza, A. / Zhang, Y. / Ledermann, R. / Tang, C. / Mikoc, A. / Ahel, I.
History
DepositionOct 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DarT ssDNA thymidine ADP-ribosyltransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0926
Polymers24,1801
Non-polymers9125
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.308, 62.308, 113.081
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein DarT ssDNA thymidine ADP-ribosyltransferase family protein


Mass: 24180.104 Da / Num. of mol.: 1 / Mutation: E152A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 4.0M Sodium Formate, 0.1M Sodium Acetate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 2→54.018 Å / Num. obs: 17764 / % possible obs: 99.9 % / Redundancy: 4.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.084 / Rrim(I) all: 0.143 / Net I/σ(I): 5.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.223 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1267 / CC1/2: 0.615 / Rpim(I) all: 0.723 / Rrim(I) all: 1.527 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
REFMAC5.8.0352refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OMW

7omw


Resolution: 2→54.018 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.176 / SU B: 14.808 / SU ML: 0.187 / Average fsc free: 0.9349 / Average fsc work: 0.947 / Cross valid method: FREE R-VALUE / ESU R: 0.179 / ESU R Free: 0.169
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2483 792 4.468 %
Rwork0.1957 16934 -
all0.198 --
obs-17726 99.73 %
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: 42.664 Å2
Baniso -1Baniso -2Baniso -3
1-0.952 Å20.476 Å20 Å2
2--0.952 Å2-0 Å2
3----3.089 Å2
Refinement stepCycle: LAST / Resolution: 2→54.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 60 131 1895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121807
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161549
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.662454
X-RAY DIFFRACTIONr_angle_other_deg0.3751.5593622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5715207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.288511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15110288
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.9591095
X-RAY DIFFRACTIONr_chiral_restr0.0530.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022032
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02369
X-RAY DIFFRACTIONr_nbd_refined0.2050.2374
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.21475
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2877
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2914
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2134
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0250.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1890.223
X-RAY DIFFRACTIONr_nbd_other0.2140.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.210
X-RAY DIFFRACTIONr_mcbond_it2.1973.664831
X-RAY DIFFRACTIONr_mcbond_other2.193.662830
X-RAY DIFFRACTIONr_mcangle_it3.4335.4851037
X-RAY DIFFRACTIONr_mcangle_other3.4345.4861038
X-RAY DIFFRACTIONr_scbond_it2.3923.891976
X-RAY DIFFRACTIONr_scbond_other2.3913.89977
X-RAY DIFFRACTIONr_scangle_it3.8485.7311417
X-RAY DIFFRACTIONr_scangle_other3.8465.7311418
X-RAY DIFFRACTIONr_lrange_it6.29450.4092120
X-RAY DIFFRACTIONr_lrange_other6.25450.2182097
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0520.428430.36912220.37112700.860.86299.60630.37
2.052-2.1080.406550.34512040.34712620.8760.88499.76230.344
2.108-2.1690.338560.31311700.31412290.9030.90799.75590.305
2.169-2.2360.37390.29911500.30111890.8760.9241000.296
2.236-2.3090.281560.28210950.28211540.9490.93899.740.275
2.309-2.390.306400.27310740.27411170.9380.94399.73140.263
2.39-2.480.332400.26310440.26510850.9280.9599.90780.252
2.48-2.5810.336480.24110010.24510500.930.95799.90480.228
2.581-2.6950.222510.229580.2210110.9630.96799.80220.206
2.695-2.8260.308580.218880.2169470.9380.96999.89440.195
2.826-2.9790.341450.2318560.2369060.9350.96699.44810.217
2.979-3.1590.237640.218010.2128650.9670.9721000.2
3.159-3.3760.311260.1878020.1918280.9410.9791000.178
3.376-3.6460.237450.1777250.187750.950.98599.35480.167
3.646-3.9920.171470.1526560.1537060.980.98699.57510.147
3.992-4.460.154180.1156400.1166580.980.9921000.107
4.46-5.1440.152120.1265620.1275740.9920.9921000.118
5.144-6.2860.224260.1454720.1495020.9750.98999.20320.137
6.286-8.830.125150.1293750.1293940.990.9998.98480.123
8.83-54.0180.20680.1522390.1532520.9580.98698.01590.148
Refinement TLS params.Method: refined / Origin x: -27.8557 Å / Origin y: 13.0148 Å / Origin z: -8.8853 Å
111213212223313233
T0.1889 Å2-0.0454 Å20.0033 Å2-0.0662 Å2-0.0095 Å2--0.0032 Å2
L0.165 °20.0854 °20.4002 °2-0.7753 °20.0689 °2--1.02 °2
S0.0133 Å °-0.0273 Å °0.0203 Å °0.0541 Å °-0.0668 Å °0.0084 Å °-0.0502 Å °-0.0499 Å °0.0535 Å °
Refinement TLS groupSelection: ALL

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