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- PDB-8bas: E. coli C7 DarT1 in complex with carba-NAD and DNA -

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Basic information

Entry
Database: PDB / ID: 8bas
TitleE. coli C7 DarT1 in complex with carba-NAD and DNA
Components
  • DNA (5'-D(*AP*AP*GP*AP*C)-3')
  • E. coli C7 DarT1
KeywordsTOXIN / TOXIN-ANTITOXIN / DNA ADP-RIBOSYLATION / ADP-ribosyltransferase activity / DNA binding
Function / homologyCARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DNA
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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 / pdbx_validate_planes
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _diffrn_source.pdbx_synchrotron_site / _pdbx_validate_planes.type
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 / pdbx_validate_planes
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_validate_planes.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E. coli C7 DarT1
C: DNA (5'-D(*AP*AP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,85211
Polymers25,6932
Non-polymers1,1599
Water4,360242
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)61.903, 61.903, 215.547
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein E. coli C7 DarT1


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) / Gene: C3F40_23400 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
#2: DNA chain DNA (5'-D(*AP*AP*GP*AP*C)-3')


Mass: 1513.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Chemical ChemComp-CNA / CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 662.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N7O13P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 4.02 Å3/Da / Density % sol: 69.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 4.0 M Sodium formate, 0.1 M Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976292 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976292 Å / Relative weight: 1
ReflectionResolution: 1.92→61.9 Å / Num. obs: 33191 / % possible obs: 100 % / Redundancy: 9.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.057 / Rrim(I) all: 0.177 / Net I/σ(I): 8.3
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 9.8 % / Rmerge(I) obs: 2.472 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2151 / CC1/2: 0.501 / Rpim(I) all: 0.818 / Rrim(I) all: 2.606 / % possible all: 100

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Processing

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

7omz


Resolution: 1.92→59.568 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.721 / SU ML: 0.093 / Cross valid method: FREE R-VALUE / ESU R: 0.102 / ESU R Free: 0.107
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.21 1660 5.013 %
Rwork0.1704 31452 -
all0.172 --
obs-33112 99.943 %
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: 34.445 Å2
Baniso -1Baniso -2Baniso -3
1-0.617 Å20 Å20 Å2
2--0.617 Å20 Å2
3----1.234 Å2
Refinement stepCycle: LAST / Resolution: 1.92→59.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 101 76 242 2123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121948
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161637
X-RAY DIFFRACTIONr_angle_refined_deg2.0351.6752661
X-RAY DIFFRACTIONr_angle_other_deg0.6011.5573833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7655213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.587511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35910292
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.4341096
X-RAY DIFFRACTIONr_chiral_restr0.0870.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022121
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02392
X-RAY DIFFRACTIONr_nbd_refined0.2340.2348
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.21599
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2897
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2933
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2195
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1340.28
X-RAY DIFFRACTIONr_nbd_other0.2020.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2490.217
X-RAY DIFFRACTIONr_mcbond_it3.2972.984837
X-RAY DIFFRACTIONr_mcbond_other3.2972.983836
X-RAY DIFFRACTIONr_mcangle_it4.3264.4471046
X-RAY DIFFRACTIONr_mcangle_other4.3244.4481047
X-RAY DIFFRACTIONr_scbond_it4.7263.4361111
X-RAY DIFFRACTIONr_scbond_other4.7273.4381112
X-RAY DIFFRACTIONr_scangle_it6.5654.9941612
X-RAY DIFFRACTIONr_scangle_other6.5634.9971613
X-RAY DIFFRACTIONr_lrange_it9.61841.832294
X-RAY DIFFRACTIONr_lrange_other9.61841.8562295
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
1.92-1.970.3391120.32522640.32623800.8890.89199.83190.328
1.97-2.0240.3281190.30522160.30623370.9060.91999.91440.306
2.024-2.0820.2711320.2721480.2722810.950.94499.95620.266
2.082-2.1460.222950.2421130.23922080.9630.9581000.232
2.146-2.2170.2561070.21820380.21921470.9450.96699.90680.207
2.217-2.2940.263910.21419960.21620870.9450.9671000.201
2.294-2.3810.2421090.18919000.19220100.9630.97599.95020.175
2.381-2.4780.2111100.18218320.18419420.9720.9781000.166
2.478-2.5880.2191030.1717570.17318610.9680.98299.94630.155
2.588-2.7140.201750.15717090.15917840.9730.9851000.141
2.714-2.8610.186870.15616020.15816890.9790.9851000.141
2.861-3.0340.209880.16115440.16416330.9680.98399.93880.148
3.034-3.2420.233750.17614670.17815430.9660.98299.93520.164
3.242-3.5010.22750.16913510.17214260.980.9851000.16
3.501-3.8340.179540.14512800.14613340.9840.9891000.136
3.834-4.2850.173600.11511460.11712060.9840.9921000.106
4.285-4.9430.156550.10210400.10510950.9870.9941000.09
4.943-6.0440.183440.1488930.1499370.9770.9881000.14
6.044-8.5040.217380.1737130.1757520.9760.98499.8670.158
8.504-59.5680.169310.1894430.1884790.9820.98198.95620.174
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2980.0233-0.42430.5147-0.03010.6384-0.0393-0.01750.00020.06520.059-0.0114-0.00890.0444-0.01960.130.00280.02680.0531-0.00360.0071-9.23068.696-34.2386
20.75840.0475-0.93440.69691.32823.92310.15830.17810.2141-0.02540.09940.0219-0.2877-0.0199-0.25770.14460.00020.05220.06880.04810.0622-6.364921.3767-43.4828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA0 - 307
2X-RAY DIFFRACTION2C1 - 5

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