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- PDB-8ce2: X-ray structure of the adduct formed upon reaction of a B-DNA dou... -

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Basic information

Entry
Database: PDB / ID: 8ce2
TitleX-ray structure of the adduct formed upon reaction of a B-DNA double helical dodecamer with dirhodium tetraacetate
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / dodecamer / dirhodium / interaction
Function / homologyRhodium / DNA / DNA (> 10)
Function and homology information
Biological speciesDNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.24 Å
AuthorsTito, G. / Troisi, R. / Ferraro, G. / Sica, F. / Merlino, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Dalton Trans / Year: 2023
Title: Dirhodium tetraacetate binding to a B-DNA double helical dodecamer probed by X-ray crystallography and mass spectrometry.
Authors: Tito, G. / Troisi, R. / Ferraro, G. / Geri, A. / Massai, L. / Messori, L. / Sica, F. / Merlino, A.
History
DepositionFeb 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5926
Polymers7,3272
Non-polymers2664
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-16 kcal/mol
Surface area4600 Å2
Unit cell
Length a, b, c (Å)25.530, 40.310, 65.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-RH / Rhodium


Mass: 102.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Rh
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 7% (v/v) 2-methyl-2,4-pentanediol, 20 mM MgCl2, 80 mM spermine tetrahydrochloride, and 60 mM sodium cacodylate at pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.24→34.36 Å / Num. obs: 19898 / % possible obs: 99.9 % / Redundancy: 10.8 % / CC1/2: 0.999 / Net I/σ(I): 23.2
Reflection shellResolution: 1.24→1.26 Å / Redundancy: 8.4 % / Num. unique obs: 996 / CC1/2: 0.785 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.24→34.36 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.89 / SU ML: 0.039 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.052
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2227 972 4.885 %
Rwork0.1971 18926 -
all0.198 --
obs-19898 99.905 %
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: 16.356 Å2
Baniso -1Baniso -2Baniso -3
1-0.665 Å20 Å2-0 Å2
2--0.468 Å20 Å2
3----1.134 Å2
Refinement stepCycle: LAST / Resolution: 1.24→34.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 4 168 658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.011544
X-RAY DIFFRACTIONr_bond_other_d0.0020.017268
X-RAY DIFFRACTIONr_angle_refined_deg3.0731.795836
X-RAY DIFFRACTIONr_angle_other_deg0.4951.55636
X-RAY DIFFRACTIONr_chiral_restr0.170.294
X-RAY DIFFRACTIONr_gen_planes_refined0.0390.02292
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0288
X-RAY DIFFRACTIONr_nbd_refined0.1530.227
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.2279
X-RAY DIFFRACTIONr_nbtor_refined0.2560.2184
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.2150
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.291
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0760.23
X-RAY DIFFRACTIONr_nbd_other0.1380.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.216
X-RAY DIFFRACTIONr_scbond_it1.9591.943544
X-RAY DIFFRACTIONr_scbond_other1.9581.943544
X-RAY DIFFRACTIONr_scangle_it2.8512.946836
X-RAY DIFFRACTIONr_scangle_other2.8492.945837
X-RAY DIFFRACTIONr_lrange_it4.52732.366806
X-RAY DIFFRACTIONr_lrange_other3.99723.371750
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
1.24-1.2720.261810.30313560.314380.9490.92699.93050.282
1.272-1.3070.287680.29513470.29514160.9350.92999.92940.263
1.307-1.3450.29600.27813200.27913800.940.9361000.244
1.345-1.3860.362720.25112320.25613040.8950.9531000.214
1.386-1.4320.284680.23812420.24113100.9450.9581000.205
1.432-1.4820.281690.2211680.22412380.9570.96799.91920.187
1.482-1.5380.215660.22211600.22112260.9720.9691000.191
1.538-1.60.24540.20611250.20711800.9670.97199.91530.181
1.6-1.6710.267490.20410470.20711010.960.97599.54590.189
1.671-1.7530.156430.18610320.18410750.9830.9771000.178
1.753-1.8470.156610.1699790.16810400.9830.9811000.168
1.847-1.9590.303410.1869290.199700.9470.9771000.191
1.959-2.0940.201410.1948730.1949140.9770.9741000.204
2.094-2.2610.265420.2068280.2098710.9470.97299.88520.223
2.261-2.4750.175300.1957570.1947870.9770.9771000.225
2.475-2.7660.28380.2046820.2087200.9430.9721000.238
2.766-3.190.281360.2046300.2086680.9470.97299.70060.256
3.19-3.8990.186200.1655270.1665470.9860.9831000.228
3.899-5.4790.169240.1774250.1764500.9830.97999.77780.24
5.479-34.360.21890.222670.222780.9710.97299.28060.306

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