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- PDB-1vti: DNA-DRUG INTERACTIONS: THE CRYSTAL STRUCTURES OF D(TGATCA) COMPLE... -

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Basic information

Entry
Database: PDB / ID: 1vti
TitleDNA-DRUG INTERACTIONS: THE CRYSTAL STRUCTURES OF D(TGATCA) COMPLEXED WITH DAUNOMYCIN
ComponentsDNA (5'-D(*TP*GP*TP*AP*CP*A)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homologyDAUNOMYCIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsNunn, C.M. / Van Meervelt, L. / Zhang, S. / Moore, M.H. / Kennard, O.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: DNA-Drug Interactions: The Crystal Structures of d(TGTACA) and d(TGATCA) Complexed with Daunomycin
Authors: Nunn, C.M. / Van Meervelt, L. / Zhang, S. / Moore, M.H. / Kennard, O.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: DNA-Drug Interactions: The Crystal Structure of d(CGATCG) Complexed with Daunomycin
Authors: Moore, M.H. / Hunter, W.N. / D'Estaintot, B.L. / Kennard, O.
History
DepositionMar 1, 1992Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,3362
Polymers1,8081
Non-polymers5281
Water93752
1
A: DNA (5'-D(*TP*GP*TP*AP*CP*A)-3')
hetero molecules

A: DNA (5'-D(*TP*GP*TP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,6714
Polymers3,6162
Non-polymers1,0552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)28.110, 28.110, 52.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 1808.229 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-DM1 / DAUNOMYCIN / DAUNORUBICIN


Mass: 527.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29NO10 / Comment: medication, chemotherapy*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, temperature 293.00K
Components of the solutions
IDConc.NameCrystal-IDDetailsSol-IDVolume (Å3)
12 WATER1311
25 MPD1614
38 MG ACETATE1917
411 SPERMINE_HCL112110
514 NA CACODYLATE115113
617 WATER118216
720 MPD121219

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Data collection

DiffractionMean temperature: 275 K
DetectorType: SYNTEX P21 / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.7 Å / Num. obs: 2626 / Observed criterion σ(I): 0

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.7→10 Å / σ(F): 3 /
RfactorNum. reflection
obs0.26 1885
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 38 52 210

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