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- PDB-1aio: CRYSTAL STRUCTURE OF A DOUBLE-STRANDED DNA CONTAINING THE MAJOR A... -

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Basic information

Entry
Database: PDB / ID: 1aio
TitleCRYSTAL STRUCTURE OF A DOUBLE-STRANDED DNA CONTAINING THE MAJOR ADDUCT OF THE ANTICANCER DRUG CISPLATIN
Components
  • DNA (5'-D(*CP*CP*(BRU)P*CP*TP*[PT(NH3)2(GP*GP)]*TP*CP*TP*CP*C)-3')
  • DNA (5'-D(*GP*GP*AP*GP*AP*CP*CP*AP*GP*AP*GP*G)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED
Function / homologyCisplatin / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsTakahara, P.M. / Rosenzweig, A.C. / Frederick, C.A. / Lippard, S.J.
Citation
Journal: Nature / Year: 1995
Title: Crystal structure of double-stranded DNA containing the major adduct of the anticancer drug cisplatin.
Authors: Takahara, P.M. / Rosenzweig, A.C. / Frederick, C.A. / Lippard, S.J.
#1: Journal: J.Am.Chem.Soc. / Year: 1996
Title: Crystal Structure of the Anticancer Drug Cisplatin Bound to Duplex DNA
Authors: Takahara, P.M. / Frederick, C.A. / Lippard, S.J.
History
DepositionApr 23, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Apr 24, 1997Provider: repository / Type: Initial release
SupersessionMay 15, 1997ID: 1GPG
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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*CP*(BRU)P*CP*TP*[PT(NH3)2(GP*GP)]*TP*CP*TP*CP*C)-3')
B: DNA (5'-D(*GP*GP*AP*GP*AP*CP*CP*AP*GP*AP*GP*G)-3')
C: DNA (5'-D(*CP*CP*(BRU)P*CP*TP*[PT(NH3)2(GP*GP)]*TP*CP*TP*CP*C)-3')
D: DNA (5'-D(*GP*GP*AP*GP*AP*CP*CP*AP*GP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3836
Polymers14,7834
Non-polymers6002
Water1,11762
1
A: DNA (5'-D(*CP*CP*(BRU)P*CP*TP*[PT(NH3)2(GP*GP)]*TP*CP*TP*CP*C)-3')
B: DNA (5'-D(*GP*GP*AP*GP*AP*CP*CP*AP*GP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6923
Polymers7,3922
Non-polymers3001
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*CP*CP*(BRU)P*CP*TP*[PT(NH3)2(GP*GP)]*TP*CP*TP*CP*C)-3')
D: DNA (5'-D(*GP*GP*AP*GP*AP*CP*CP*AP*GP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6923
Polymers7,3922
Non-polymers3001
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.270, 35.460, 47.010
Angle α, β, γ (deg.)79.81, 84.75, 82.79
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain DNA (5'-D(*CP*CP*(BRU)P*CP*TP*[PT(NH3)2(GP*GP)]*TP*CP*TP*CP*C)-3')


Mass: 3630.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#2: DNA chain DNA (5'-D(*GP*GP*AP*GP*AP*CP*CP*AP*GP*AP*GP*G)-3')


Mass: 3761.468 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#3: Chemical ChemComp-CPT / Cisplatin / diammine(dichloro)platinum


Mass: 300.045 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 4

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5[CO(NH3)6]CL311
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 mMDNA1drop
252 mMcacodylate acid1drop
315 mM1dropMgCl2
46 mM1drop[Co(NH3)6]Cl3
53 %MPD1drop
65 %MPD1reservoir
71

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Data collection

DiffractionMean temperature: 277 K
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→8 Å / Num. obs: 5797 / Observed criterion σ(I): 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 8 Å / % possible obs: 97 % / Rmerge(I) obs: 0.062

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.6→8 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.251 579 10 %RANDOM
Rwork0.206 ---
obs0.206 5797 97 %-
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 972 6 62 1040
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 8 Å / σ(F): 1 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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