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- PDB-3co3: X-Ray Crystal Structure of a Monofunctional Platinum-DNA Adduct, ... -

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Basic information

Entry
Database: PDB / ID: 3co3
TitleX-Ray Crystal Structure of a Monofunctional Platinum-DNA Adduct, cis-{Pt(NH3)2(pyridine)}2+ Bound to Deoxyguanosine in a Dodecamer Duplex
Components
  • 5'-D(*DCP*DCP*DTP*DCP*DTP*DCP*DGP*DTP*DCP*DTP*DCP*DC)-3'
  • 5'-D(*DGP*DGP*DAP*DGP*DAP*DCP*DGP*DAP*DGP*DAP*DGP*DG)-3'
KeywordsDNA / PLATINUM-DNA DUPLEX / CISPLATIN / MONOFUNCTIONAL PT COMPOUND
Function / homologycis-diammine(pyridine)chloroplatinum(II) / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.16 Å
AuthorsLovejoy, K.S. / Todd, R.C. / Zhang, S. / McCormick, M.S. / D'Aquino, J.A. / Reardon, J.T. / Sancar, A. / Giacomini, K.M. / Lippard, S.J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: cis-Diammine(pyridine)chloroplatinum(II), a monofunctional platinum(II) antitumor agent: Uptake, structure, function, and prospects.
Authors: Lovejoy, K.S. / Todd, R.C. / Zhang, S. / McCormick, M.S. / D'Aquino, J.A. / Reardon, J.T. / Sancar, A. / Giacomini, K.M. / Lippard, S.J.
History
DepositionMar 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*DCP*DCP*DTP*DCP*DTP*DCP*DGP*DTP*DCP*DTP*DCP*DC)-3'
B: 5'-D(*DGP*DGP*DAP*DGP*DAP*DCP*DGP*DAP*DGP*DAP*DGP*DG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6703
Polymers7,3272
Non-polymers3441
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.440, 66.010, 56.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: DNA chain 5'-D(*DCP*DCP*DTP*DCP*DTP*DCP*DGP*DTP*DCP*DTP*DCP*DC)-3'


Mass: 3525.292 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*DGP*DGP*DAP*DGP*DAP*DCP*DGP*DAP*DGP*DAP*DGP*DG)-3'


Mass: 3801.492 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-C7P / cis-diammine(pyridine)chloroplatinum(II)


Mass: 343.692 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11ClN3Pt
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsC7P IS AN ANTITUMOR AGENT BOUND TO DG 7 A.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 120 mM Mg(acetate), 50 mM Na cacodylate, 1 mM spermine, 28% w/v PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1Mg(acetate)11
2Na cacodylate11
3spermine11
4PEG400011
5H2O11
6Mg(acetate)12
7Na cacodylate12
8spermine12
9PEG400012
10H2O12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C11.072
SYNCHROTRONSSRL BL9-220.984
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDApr 4, 2007
MARMOSAIC 325 mm CCD2CCDJul 5, 2007Flat collimating mirror, toroid focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Double crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0721
20.9841
ReflectionRedundancy: 6.3 % / Av σ(I) over netI: 23.2 / Number: 26784 / Rmerge(I) obs: 0.073 / Χ2: 7.54 / D res high: 2.72 Å / D res low: 50 Å / Num. obs: 4231 / % possible obs: 94.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.865095.610.0517.4767.2
4.655.8699.610.0586.2347.4
4.064.6510010.0685.6217.5
3.694.0610010.0866.5827.6
3.433.6999.810.10411.7477.4
3.223.4392.910.13118.2667
3.063.2299.810.1224.156
2.933.0694.310.1351.9645
2.822.9386.310.1391.4613.9
2.722.8273.610.1761.5373.1
ReflectionResolution: 2.17→50 Å / Num. all: 4836 / Num. obs: 4765 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.107 / Χ2: 0.989 / Net I/σ(I): 18.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.17-2.256.80.5563670.65276
2.25-2.346.10.5764651.27697.9
2.34-2.447.20.2324970.645100
2.44-2.577.30.1754861.102100
2.57-2.737.20.1264901.054100
2.73-2.957.20.1094911.065100
2.95-3.247.20.1074851.03100
3.24-3.7170.0934841.0295.3
3.71-4.676.80.0944990.9998.6
4.67-506.30.1065011.02692.1

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Phasing

PhasingMethod: SAD
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_12.7233.19001887442
ANO_12.7233.193.83018390
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_17.96-33.19005845
ISO_15.71-7.960012550
ISO_14.68-5.710017249
ISO_14.07-4.680020252
ISO_13.64-4.070023151
ISO_13.33-3.640025844
ISO_13.08-3.330026854
ISO_12.89-3.080029745
ISO_12.72-2.890027652
ANO_17.96-33.198.3350550
ANO_15.71-7.966.43101250
ANO_14.68-5.714.66601720
ANO_14.07-4.683.54802020
ANO_13.64-4.072.81202310
ANO_13.33-3.642.29702570
ANO_13.08-3.331.81502670
ANO_12.89-3.081.42502860
ANO_12.72-2.890.99102440
Phasing MAD set siteCartn x: 17.103 Å / Cartn y: 4.064 Å / Cartn z: 7.169 Å / Atom type symbol: PT / B iso: 86.63 / Occupancy: 0.91

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.16→28.44 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.136 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.234 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.254 216 4.7 %RANDOM
Rwork0.225 ---
all0.248 4836 --
obs0.227 4614 95.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.444 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.16→28.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 9 16 511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021554
X-RAY DIFFRACTIONr_angle_refined_deg1.4353844
X-RAY DIFFRACTIONr_chiral_restr0.0890.294
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02254
X-RAY DIFFRACTIONr_nbd_refined0.2130.287
X-RAY DIFFRACTIONr_nbtor_refined0.3490.2307
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.25
X-RAY DIFFRACTIONr_mcbond_it6.1681.52
X-RAY DIFFRACTIONr_scbond_it5.8633792
X-RAY DIFFRACTIONr_scangle_it7.3874.5844
LS refinement shellResolution: 2.162→2.218 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 12 -
Rwork0.443 274 -
all-286 -
obs--81.48 %

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