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- PDB-1r68: Role of the amino sugar in DNA binding of disaccharide anthracycl... -

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Basic information

Entry
Database: PDB / ID: 1r68
TitleRole of the amino sugar in DNA binding of disaccharide anthracyclines: crystal structure of MAR70/d(CGATCG) complex
Components5'-D(*CP*GP*AP*TP*CP*G)-3'
KeywordsDNA / right handed DNA / double helix / drug-DNA complex
Function / homology4'-EPI-4'-(2-DEOXYFUCOSE)DAUNOMYCIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsTemperini, C. / Cirilli, M. / Aschi, M. / Ughetto, G.
Citation
Journal: BIOORG.MED.CHEM. / Year: 2005
Title: Role of the amino sugar in DNA binding of disaccharide anthracyclines: crystal structure of the complex MAR70/d(CGATCG).
Authors: Temperini, C. / Cirilli, M. / Aschi, M. / Ughetto, G.
#1: Journal: Nucleic Acids Res. / Year: 2003
Title: The crystal structure of the complex between a disaccharide anthracycline and the DNA hexamer d(CGATCG) reveals two different binding sites involving two DNA duplexes
Authors: Temperini, C. / Messori, L. / Orioli, P. / Di Bugno, C. / Animati, F. / Ughetto, G.
History
DepositionOct 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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: 5'-D(*CP*GP*AP*TP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,4672
Polymers1,8091
Non-polymers6581
Water37821
1
A: 5'-D(*CP*GP*AP*TP*CP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)4,9344
Polymers3,6182
Non-polymers1,3152
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)28.190, 28.190, 53.250
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 5'-D(*CP*GP*AP*TP*CP*G)-3'


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-MAR / 4'-EPI-4'-(2-DEOXYFUCOSE)DAUNOMYCIN / MAR70 / DAUNOMYCIN DERIVATIVE


Mass: 657.662 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H39NO13
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 298 K / pH: 6
Details: Magnesium chloride, cacodylate, spermine, MPD, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 6.00
Components of the solutions
IDNameCrystal-IDSol-ID
1Magnesium chloride11
2cacodylate11
3spermine11
4MPD11
5H2O11
6Magnesium chloride12
7cacodylate12
8spermine12
9MPD12
10H2O12

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER / Date: Feb 15, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.2→15 Å / Num. obs: 6369 / % possible obs: 97.8 % / Biso Wilson estimate: 15.34 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 4.3
Reflection shellResolution: 1.2→1.3 Å / % possible all: 87

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Processing

Software
NameClassification
TEXANdata collection
TEXANdata reduction
AMoREphasing
SHELXL-97refinement
TEXSANdata reduction
TEXSANdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→10 Å / σ(F): 4 /
% reflectionSelection details
obs97.8 %-
Rfree-RANDOM
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 47 21 188
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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