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- PDB-1a2e: CRYSTAL STRUCTURE OF A DOUBLE-STRANDED DNA DECAMER CONTAINING A C... -

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Basic information

Entry
Database: PDB / ID: 1a2e
TitleCRYSTAL STRUCTURE OF A DOUBLE-STRANDED DNA DECAMER CONTAINING A CISPLATIN INTERSTRAND CROSS-LINK ADDUCT
Components
  • DNA (5'-D(*CP*CP*TP*CP*GP*CP*TP*CP*TP*C)-3')
  • DNA (5'-D(*GP*AP*GP*AP*GP*CP*GP*AP*GP*G)-3')
KeywordsDNA / ANTITUMOR DRUG / CIS-DDP / INTERSTRAND CROSS-LINK
Function / homologyCisplatin / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.63 Å
AuthorsCoste, F. / Zelwer, C.
CitationJournal: Nucleic Acids Res. / Year: 1999
Title: Crystal structure of a double-stranded DNA containing a cisplatin interstrand cross-link at 1.63 A resolution: hydration at the platinated site.
Authors: Coste, F. / Malinge, J.M. / Serre, L. / Shepard, W. / Roth, M. / Leng, M. / Zelwer, C.
History
DepositionJan 5, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Apr 12, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,3913
Polymers6,0912
Non-polymers3001
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.890, 29.980, 46.570
Angle α, β, γ (deg.)90.00, 95.98, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

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


Mass: 2931.917 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PT(CPT) CROSSLINKS N7(G5) AND N7(G15)
#2: DNA chain DNA (5'-D(*GP*AP*GP*AP*GP*CP*GP*AP*GP*G)-3')


Mass: 3159.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PT(CPT) CROSSLINKS N7(G5) AND N7(G15)
#3: Chemical ChemComp-CPT / Cisplatin / diammine(dichloro)platinum


Mass: 300.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 56 %
Crystal growpH: 6.2 / Details: pH 6.20
Crystal
*PLUS
Density % sol: 56 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.0825 MDNA1drop
220 mMsodium cacodylate1drop
35 mM1dropNaCl
430 mM1dropKCl
52.5 mMspermine1drop
62 %(v/v)MPD1drop
7MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW21B / Wavelength: 1.0711
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1997 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0711 Å / Relative weight: 1
ReflectionResolution: 1.63→46.13 Å / Num. obs: 7353 / % possible obs: 93.1 % / Observed criterion σ(I): 4 / Redundancy: 3.5 % / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 6
Reflection shellResolution: 1.63→1.72 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.063 / Mean I/σ(I) obs: 12 / Rsym value: 0.049 / % possible all: 91
Reflection
*PLUS
Num. obs: 7333 / % possible obs: 97 % / Num. measured all: 60517
Reflection shell
*PLUS
Redundancy: 3.1 % / Mean I/σ(I) obs: 11.1

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Processing

Software
NameVersionClassification
SHARPphasing
SHELXL-96refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.63→20 Å / Num. parameters: 2176 / Num. restraintsaints: 2201 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: NUCLSQ
RfactorNum. reflection% reflection
all0.1692 6983 -
obs0.1692 6983 93.1 %
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-223
Refine analyzeOccupancy sum hydrogen: 479.67
Refinement stepCycle: LAST / Resolution: 1.63→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 3 92 499
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.026
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.062
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.009
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.098
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.016

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