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- PDB-8ri5: Crystal structure of transplatin/B-DNA adduct obtained upon 48 h ... -

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Basic information

Entry
Database: PDB / ID: 8ri5
TitleCrystal structure of transplatin/B-DNA adduct obtained upon 48 h of soaking
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / dodecamer / dickerson / platinum / interaction
Function / homologyAMMONIA / : / DNA / DNA (> 10)
Function and homology information
Biological speciesDNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.415 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 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)7,5635
Polymers7,3272
Non-polymers2363
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-33 kcal/mol
Surface area4450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.474, 40.221, 65.676
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-NH3 / AMMONIA / Ammonia


Mass: 17.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH3
#4: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
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: 1.41→25.47 Å / Num. obs: 12070 / % possible obs: 89.9 % / Redundancy: 10 % / CC1/2: 0.999 / Net I/σ(I): 30.5
Reflection shellResolution: 1.41→1.45 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 490 / CC1/2: 0.832 / % possible all: 51.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.415→25.45 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.161 / SU ML: 0.046 / Cross valid method: FREE R-VALUE / ESU R: 0.074 / ESU R Free: 0.079
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2295 601 4.99 %
Rwork0.1897 11444 -
all0.192 --
obs-12045 89.474 %
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: 17.203 Å2
Baniso -1Baniso -2Baniso -3
1-0.765 Å20 Å2-0 Å2
2--0.262 Å20 Å2
3----1.027 Å2
Refinement stepCycle: LAST / Resolution: 1.415→25.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 3 121 610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.011544
X-RAY DIFFRACTIONr_bond_other_d0.0020.017268
X-RAY DIFFRACTIONr_angle_refined_deg3.1991.795836
X-RAY DIFFRACTIONr_angle_other_deg0.4841.55636
X-RAY DIFFRACTIONr_chiral_restr0.1620.294
X-RAY DIFFRACTIONr_gen_planes_refined0.0360.02292
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0288
X-RAY DIFFRACTIONr_nbd_refined0.1510.231
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.2276
X-RAY DIFFRACTIONr_nbtor_refined0.2520.2184
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.2148
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.272
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0650.24
X-RAY DIFFRACTIONr_nbd_other0.1440.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1470.213
X-RAY DIFFRACTIONr_scbond_it2.0452.019544
X-RAY DIFFRACTIONr_scbond_other2.0452.02544
X-RAY DIFFRACTIONr_scangle_it3.0053.062836
X-RAY DIFFRACTIONr_scangle_other3.0033.061837
X-RAY DIFFRACTIONr_lrange_it4.72330.744788
X-RAY DIFFRACTIONr_lrange_other4.21926.57751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.415-1.4520.311240.249466X-RAY DIFFRACTION50.7246
1.452-1.4910.278280.221527X-RAY DIFFRACTION58.0544
1.491-1.5340.259320.209606X-RAY DIFFRACTION69.6507
1.534-1.5810.232380.21720X-RAY DIFFRACTION84.3159
1.581-1.6330.227410.206774X-RAY DIFFRACTION94.9883
1.633-1.690.215420.183801X-RAY DIFFRACTION97.9094
1.69-1.7540.198410.173765X-RAY DIFFRACTION99.139
1.754-1.8250.165390.164738X-RAY DIFFRACTION98.6041
1.825-1.9060.241370.172718X-RAY DIFFRACTION99.473
1.906-1.9980.216360.194676X-RAY DIFFRACTION99.1643
1.998-2.1050.27340.176655X-RAY DIFFRACTION99.5665
2.105-2.2320.271330.194623X-RAY DIFFRACTION99.5448
2.232-2.3850.266310.199588X-RAY DIFFRACTION99.1987
2.385-2.5740.284290.192549X-RAY DIFFRACTION99.1424
2.574-2.8170.25270.201522X-RAY DIFFRACTION99.8182
2.817-3.1450.243240.209461X-RAY DIFFRACTION100
3.145-3.6220.174220.164425X-RAY DIFFRACTION99.5546
3.622-4.4140.208200.159356X-RAY DIFFRACTION99.2084
4.414-6.150.327130.206287X-RAY DIFFRACTION98.6842
6.15-100.176100.176187X-RAY DIFFRACTION98.0099

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