3LPV | pdb_00003lpv

X-ray crystal structure of duplex DNA containing a cisplatin 1,2-d(GpG) intrastrand cross-link

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2010-02-06 Released: 2010-08-11 
  • Deposition Author(s): Todd, R.C., Lippard, S.J.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 
    0.198 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 

Literature

Structure of duplex DNA containing the cisplatin 1,2-{Pt(NH(3))(2)}(2+)-d(GpG) cross-link at 1.77A resolution.

Todd, R.C., Lippard, S.J.

(2010) J Inorg Biochem 104: 902-908

  • DOI: https://doi.org/10.1016/j.jinorgbio.2010.04.005
  • Primary Citation Related Structures: 
    3LPV

  • PubMed Abstract: 

    We report the 1.77-A resolution X-ray crystal structure of a dodecamer DNA duplex with the sequence 5'-CCTCTGGTCTCC-3' that has been modified to contain a single engineered 1,2-cis-{Pt(NH(3))(2)}(2+)-d(GpG) cross-link, the major DNA adduct of cisplatin. These data represent a significant improvement in resolution over the previously published 2.6-A structure. The ammine ligands in this structure are clearly resolved, leading to improved visualization of the cross-link geometry with respect to both the platinum center and to the nucleobases, which adopt a higher energy conformation. Also better resolved are the deoxyribose sugar puckers, which allow us to re-examine the global structure of platinum-modified DNA. Another new feature of this model is the location of four octahedral [Mg(H(2)O)(6)](2+) ions associated with bases in the DNA major groove and the identification of 124 ordered water molecules that participate in hydrogen-bonding interactions with either the nucleic acid or the diammineplatinum(II) moiety.

    • Organizational Affiliation: 
    • Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.

Macromolecule Content 

  • Total Structure Weight: 15.35 kDa 
  • Atom Count: 1,130 
  • Modeled Residue Count: 48 
  • Deposited Residue Count: 48 
  • Unique nucleic acid chains: 2

Macromolecules

Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*CP*CP*TP*CP*TP*GP*GP*TP*CP*TP*CP*C)-3'
A, C
12N/A
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*GP*GP*AP*GP*AP*CP*CP*AP*GP*AP*GP*G)-3'
B, D
12N/A
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free:  0.198 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.303α = 80.06
b = 35.425β = 84.09
c = 45.128γ = 81.77
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description