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- PDB-8ri3: Crystal structure of transplatin/B-DNA adduct obtained upon 7 day... -

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Basic information

Entry
Database: PDB / ID: 8ri3
TitleCrystal structure of transplatin/B-DNA adduct obtained upon 7 days of soaking
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / dodecamer / platin / interaction
Function / homologyAMMONIA / : / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTito, G. / Troisi, R. / Ferraro, G. / Sica, F. / Merlino, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Dalton Trans / Year: 2024
Title: On the mechanism of action of arsenoplatins: arsenoplatin-1 binding to a B-DNA dodecamer.
Authors: Troisi, R. / Tito, G. / Ferraro, G. / Sica, F. / Massai, L. / Geri, A. / Cirri, D. / Messori, L. / Merlino, A.
History
DepositionDec 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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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)8,02310
Polymers7,3272
Non-polymers6968
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-92 kcal/mol
Surface area4230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.560, 40.390, 65.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 1 types, 2 molecules AB

#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.) synthetic construct (others)

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Non-polymers , 5 types, 117 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pt / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NH3 / AMMONIA / Ammonia


Mass: 17.031 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NH3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 46.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 7-14% (v/v) 2-methyl-2,4-pentanediol (MPD), 20 mM MgCl2, 80 mM spermine tetrahydrochloride, and 60 mM sodium cacodylate 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: Oct 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→34.404 Å / Num. obs: 13972 / % possible obs: 98.9 % / Redundancy: 9.7 % / CC1/2: 0.998 / Net I/σ(I): 13.2
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 698 / CC1/2: 0.601 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→34.404 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.281 / WRfactor Rwork: 0.226 / SU B: 1.772 / SU ML: 0.066 / Average fsc free: 0.9374 / Average fsc work: 0.9574 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.086
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2567 591 4.793 %
Rwork0.2159 11739 -
all0.218 --
obs-12330 88.141 %
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: 15.483 Å2
Baniso -1Baniso -2Baniso -3
1-0.058 Å2-0 Å20 Å2
2---0.149 Å2-0 Å2
3---0.091 Å2
Refinement stepCycle: LAST / Resolution: 1.4→34.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 8 109 603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.011547
X-RAY DIFFRACTIONr_bond_other_d0.0020.017271
X-RAY DIFFRACTIONr_ext_dist_refined_b00.0014
X-RAY DIFFRACTIONr_angle_refined_deg3.0461.784841
X-RAY DIFFRACTIONr_angle_other_deg0.4941.557639
X-RAY DIFFRACTIONr_chiral_restr0.1490.294
X-RAY DIFFRACTIONr_gen_planes_refined0.030.02292
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0288
X-RAY DIFFRACTIONr_nbd_refined0.2490.243
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.2288
X-RAY DIFFRACTIONr_nbtor_refined0.2450.2199
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0960.2138
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.260
X-RAY DIFFRACTIONr_metal_ion_refined0.0950.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0490.23
X-RAY DIFFRACTIONr_nbd_other0.1550.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1150.29
X-RAY DIFFRACTIONr_scbond_it2.4051.774547
X-RAY DIFFRACTIONr_scbond_other1.9771.767546
X-RAY DIFFRACTIONr_scangle_it3.7122.68845
X-RAY DIFFRACTIONr_scangle_other3.7082.678845
X-RAY DIFFRACTIONr_lrange_it5.53123.011798
X-RAY DIFFRACTIONr_lrange_other5.41220.564771
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
1.4-1.4360.298170.3133810.31310020.9280.92439.72060.297
1.436-1.4760.381240.34810.3049720.8890.92951.95470.28
1.476-1.5180.366320.3156120.3179690.8650.92166.46030.281
1.518-1.5650.395450.2937780.2989310.9010.92988.39960.245
1.565-1.6160.439380.3317780.3369090.8280.91789.7690.268
1.616-1.6730.291370.278400.2718860.9590.95398.98420.226
1.673-1.7360.311410.237950.2348430.950.96399.16960.184
1.736-1.8060.206410.2137780.2138280.970.9798.9130.184
1.806-1.8860.33510.2267220.2337830.9410.96598.72290.194
1.886-1.9780.249280.2437250.2437620.9630.96398.81890.218
1.978-2.0850.263360.2116820.2137190.9470.97199.86090.202
2.085-2.2110.228300.1926410.1936750.9670.97599.40740.184
2.211-2.3630.241350.2026170.2046530.9620.97499.84690.202
2.363-2.5510.284270.1975800.2016080.9590.97599.83550.208
2.551-2.7930.296200.2095380.2125580.9510.9721000.232
2.793-3.120.292200.2195000.2215200.9360.9691000.258
3.12-3.5980.223210.184300.1834530.9810.98499.55850.242
3.598-4.3950.196220.1593750.1613980.9780.98499.74870.207
4.395-6.1650.218190.232920.233130.9860.97199.3610.31
6.165-34.4040.20570.2511920.2492030.9780.9698.02960.338

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