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- PDB-1d11: INTERACTIONS BETWEEN AN ANTHRACYCLINE ANTIBIOTIC AND DNA MOLECULA... -

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Basic information

Entry
Database: PDB / ID: 1d11
TitleINTERACTIONS BETWEEN AN ANTHRACYCLINE ANTIBIOTIC AND DNA MOLECULAR STRUCTURE OF DAUNOMYCIN COMPLEXED TO D(CPGPTPAPCPG) AT 1.2-ANGSTROMS RESOLUTION
ComponentsDNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homologyDAUNOMYCIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.18 Å
AuthorsWang, A.H.-J. / Ughetto, G. / Quigley, G.J. / Rich, A.
CitationJournal: Biochemistry / Year: 1987
Title: Interactions between an anthracycline antibiotic and DNA: molecular structure of daunomycin complexed to d(CpGpTpApCpG) at 1.2-A resolution.
Authors: Wang, A.H. / Ughetto, G. / Quigley, G.J. / Rich, A.
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 15, 2017Group: Structure summary
Revision 1.4Feb 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_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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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*GP*TP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,3603
Polymers1,8091
Non-polymers5512
Water1,51384
1
A: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)4,7196
Polymers3,6182
Non-polymers1,1014
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)27.860, 27.860, 52.720
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*TP*AP*CP*G)-3')


Mass: 1809.217 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: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growMethod: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE11
5NA CACODYLATE11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 6.5 / Method: other
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.UnitCommon nameChemical formulaSol-IDDetails
22 mMdaunomycin
315 mMMgCl2
410 mMspermine
530 mMcacodylate
65 %MPD1
730 %(v/v)
1mMDNA hexamersingle strand

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Data collection

DiffractionMean temperature: 288 K
DetectorType: NICOLET P3X / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.2 Å / Num. all: 13258 / Num. obs: 9238 / Observed criterion σ(F): 2

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.18→10 Å / σ(F): 3 /
RfactorNum. reflection
obs0.175 5133
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.18→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 39 84 243
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.034
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it
X-RAY DIFFRACTIONn_sugar_angle_it
X-RAY DIFFRACTIONn_phos_bond_it
X-RAY DIFFRACTIONn_phos_angle_it
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d
X-RAY DIFFRACTIONn_sugar_bond_angle_d
X-RAY DIFFRACTIONn_phos_bond_d
X-RAY DIFFRACTIONn_phos_bond_angle_d
X-RAY DIFFRACTIONn_plane_restr
X-RAY DIFFRACTIONn_chiral_restr
X-RAY DIFFRACTIONn_singtor_nbd
X-RAY DIFFRACTIONn_multtor_nbd
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 1.2 Å / Num. reflection obs: 5133 / σ(F): 3 / Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.8 Å2
Refine LS restraints
*PLUS
Type: n_bond_d

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