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- PDB-1da0: DNA-DRUG INTERACTIONS: THE CRYSTAL STRUCTURE OF D(CGATCG) COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 1da0
TitleDNA-DRUG INTERACTIONS: THE CRYSTAL STRUCTURE OF D(CGATCG) COMPLEXED WITH DAUNOMYCIN
ComponentsDNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homologyDAUNOMYCIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsMoore, M.H. / Hunter, W.N. / Langlois D'Estaintot, B. / Kennard, O.
CitationJournal: 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
DepositionOct 17, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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_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: DNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,3372
Polymers1,8091
Non-polymers5281
Water0
1
A: DNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)4,6734
Polymers3,6182
Non-polymers1,0552
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)27.980, 27.980, 52.870
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(*CP*GP*AP*TP*CP*G)-3')


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-DM1 / DAUNOMYCIN / DAUNORUBICIN / Daunorubicin


Mass: 527.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29NO10 / Comment: medication, chemotherapy*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, temperature 293.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MG ACETATE11
4SPERMINE_HCL11
5NA CACODYLATE11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.5 mMd(CGATCG)1dropsingle stranded
21.5 mMdaunomycin hydrochloride1drop
320 mMmagnesium acetate1drop
43.5 mMspermine hydrochloride1drop
520 mMsodium cacodylate1drop
69 %(v/v)MPD1drop
750 %(v/v)1reservoir

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Data collection

DiffractionMean temperature: 277 K
DetectorType: SYNTEX P21 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.5 Å / Num. all: 3529 / Num. obs: 2801 / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.09
Reflection
*PLUS
Highest resolution: 1.5 Å / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.09

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.5→10 Å / σ(F): 5 /
RfactorNum. reflection
obs0.25 1845
Refine Biso Class: ALL ATOMS / Details: TR / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 38 0 158
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 10 Å / σ(F): 5 / Num. reflection obs: 1845 / Rfactor obs: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS

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