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- PDB-1d12: STRUCTURAL COMPARISON OF ANTICANCER DRUG-DNA COMPLEXES. ADRIAMYCI... -

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Basic information

Entry
Database: PDB / ID: 1d12
TitleSTRUCTURAL COMPARISON OF ANTICANCER DRUG-DNA COMPLEXES. ADRIAMYCIN AND DAUNOMYCIN
ComponentsDNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homologyDOXORUBICIN / SPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsFrederick, C.A. / Williams, L.D. / Ughetto, G. / Van Der Marel, G.A. / Van Boom, J.H. / Rich, A. / Wang, A.H.-J.
CitationJournal: Biochemistry / Year: 1990
Title: Structural comparison of anticancer drug-DNA complexes: adriamycin and daunomycin.
Authors: Frederick, C.A. / Williams, L.D. / Ughetto, G. / van der Marel, G.A. / van Boom, J.H. / Rich, A. / Wang, A.H.
History
DepositionOct 20, 1989Deposition site: BNL / Processing site: BNL
Revision 1.0Oct 15, 1990Provider: 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

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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)2,5784
Polymers1,8091
Non-polymers7693
Water1,00956
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)5,1568
Polymers3,6182
Non-polymers1,5386
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)28.210, 28.210, 53.190
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-DM2 / DOXORUBICIN / ADRIAMYCIN


Mass: 543.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29NO11
#3: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE11
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.UnitCommon nameSol-IDChemical formulaDetails
220 mMsodium cacodylatedrop
315 mMdropMgCl2
410 mMsperminedrop
55 %MPDdrop
630 %MPDreservoir
1mMDNAdropsingle strand

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Data collection

DiffractionMean temperature: 288 K
DetectorDetector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.7 Å / Observed criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 1.7 Å / Observed criterion σ(F): 2

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.7→10 Å / σ(F): 2 /
RfactorNum. reflection
obs0.177 1706
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 54 56 230
Refinement
*PLUS
σ(F): 2 / Highest resolution: 1.7 Å / Lowest resolution: 10 Å / Num. reflection obs: 1706 / Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: n_bond_d / Dev ideal: 0.028

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