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- PDB-1d54: ANTHRACYCLINE BINDING TO DNA: HIGH RESOLUTION STRUCTURE OF D(TGTA... -

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Basic information

Entry
Database: PDB / ID: 1d54
TitleANTHRACYCLINE BINDING TO DNA: HIGH RESOLUTION STRUCTURE OF D(TGTACA) COMPLEXED WITH 4'-EPIADRIAMYCIN
ComponentsDNA (5'-D(*TP*GP*TP*AP*CP*A)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homology4'-EPIDOXORUBICIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsLeonard, G.A. / Brown, T. / Hunter, W.N.
CitationJournal: Eur.J.Biochem. / Year: 1992
Title: Anthracycline binding to DNA. High-resolution structure of d(TGTACA) complexed with 4'-epiadriamycin.
Authors: Leonard, G.A. / Brown, T. / Hunter, W.N.
History
DepositionJan 6, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 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(*TP*GP*TP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,3532
Polymers1,8081
Non-polymers5451
Water59433
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)4,7064
Polymers3,6162
Non-polymers1,0892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)28.020, 28.020, 52.930
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-DM6 / 4'-EPIDOXORUBICIN / 4'-EPIADRIAMYCIN


Mass: 544.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H30NO11
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.87 Å3/Da / Density % sol: 57.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MG ACETATE11
5SPERMINE_HCL11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMDNA1drop
21.2 mM4'-epiadriamycin1drop
350 mMsodium cacodylate1drop
4140 mMmagnesium acetate1drop
50.6 mMspermine hydrochloride1drop
618 %MPD1drop
780 %1reservoir

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU AFC-5 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. all: 11022 / Num. obs: 5644
Reflection
*PLUS
Highest resolution: 1.3 Å / Num. measured all: 11022 / Rmerge(I) obs: 0.064

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.4→7 Å / σ(F): 3 /
RfactorNum. reflection
obs0.17 2381
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
ALL DRUG ATOMSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.4→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 39 33 192
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d
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_d0.014
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.033
X-RAY DIFFRACTIONn_phos_bond_d0.02
X-RAY DIFFRACTIONn_phos_bond_angle_d0.036
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: 1.4 Å / Lowest resolution: 7 Å / σ(F): 3
Solvent computation
*PLUS
Displacement parameters
*PLUS

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