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- PDB-1nab: The crystal structure of the complex between a disaccharide anthr... -

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Basic information

Entry
Database: PDB / ID: 1nab
TitleThe crystal structure of the complex between a disaccharide anthracycline and the DNA hexamer d(CGATCG) reveals two different binding sites involving two DNA duplexes
Components5'-D(*CP*GP*AP*TP*CP*G)-3'
KeywordsDNA / right handed dna / double helix / complexed with drug
Function / homologyChem-44D / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsTemperini, C. / Messori, L. / Orioli, P. / Di Bugno, C. / Animati, F. / Ughetto, G.
Citation
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.
#1: Journal: 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
DepositionNov 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2012Group: Derived calculations
Revision 1.4Feb 14, 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: 5'-D(*CP*GP*AP*TP*CP*G)-3'
B: 5'-D(*CP*GP*AP*TP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9064
Polymers3,6182
Non-polymers1,2872
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.813, 37.813, 63.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: DNA chain 5'-D(*CP*GP*AP*TP*CP*G)-3'


Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: automatic synthesis
#2: Chemical ChemComp-44D / 7-[5-(4-AMINO-5-HYDROXY-6-METHYL-TETRAHYDRO-PYRAN-2-YLOXY)-4-HYDROXY-6-METHYL-TETRAHYDRO-PYRAN-2-YLOXY]-6,9,11-TRIHYDROXY-9-(2-HYDROXY-ACETYL)-7,8,9,10-TETRAHYDRO-NAPHTHACENE-5,12-DIONE / 4'-(O-ALPHA-L-DAUNOSAMINYL)-4-DEMETHOXYDOXORUBICIN


Mass: 643.635 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H37NO13
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.11 Å3/Da / Density % sol: 60.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: magnesium chloride, cacodylate, spermine hydrochloride, MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1magnesium chloride11
2cacodylate11
3spermine hydrochloride11
4MPD11
5magnesium chloride12
6MPD12
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
140 mMsodium cacodylate1droppH6.5
20.9 mMDNA1drop
34.2 mM1dropMgCl2
48.3 mMspermine hydrocloride1drop
52 mMMEN 107551drop
760 %MPD1reservoir
61drop20%(by vol)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.03 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 27, 2001 / Details: mirrors
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.15→18.9 Å / Num. all: 28812 / Num. obs: 28737 / % possible obs: 95.4 % / Observed criterion σ(I): 1 / Redundancy: 10.9 % / Biso Wilson estimate: 41.56 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 5.4
Reflection shellResolution: 2.1→2.17 Å / Rmerge(I) obs: 0.0874 / % possible all: 75.6
Reflection
*PLUS
Lowest resolution: 8 Å / Num. obs: 2621
Reflection shell
*PLUS
Highest resolution: 2.15 Å / % possible obs: 75.6 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 1.37

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
NUCLSQrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Hendrickson, W.A.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 216 -random
Rwork0.224 ---
all0.266 2621 --
obs0.226 2321 69.7 %-
Refinement stepCycle: LAST / Resolution: 2.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 92 35 367
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.13
LS refinement shellResolution: 2→2.2 Å /
Rfactor% reflection
Rwork0.455 -
obs-3.7 %
Refinement
*PLUS
Lowest resolution: 8 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 2.17 Å

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