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- PDB-110d: ANTHRACYCLINE-DNA INTERACTIONS AT UNFAVOURABLE BASE BASE-PAIR TRI... -

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Basic information

Entry
Database: PDB / ID: 110d
TitleANTHRACYCLINE-DNA INTERACTIONS AT UNFAVOURABLE BASE BASE-PAIR TRIPLET-BINDING SITES: STRUCTURES OF D(CGGCCG)/DAUNOMYCIN AND D(TGGCCA)/ADRIAMYCIN COMPL
ComponentsDNA (5'-D(*CP*GP*GP*CP*CP*G)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homologyDAUNOMYCIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsLeonard, G.A. / Hambley, T.W. / McAuley-Hecht, K. / Brown, T. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Anthracycline-DNA interactions at unfavourable base-pair triplet-binding sites: structures of d(CGGCCG)/daunomycin and d(TGGCCA)/adriamycin complexes.
Authors: Leonard, G.A. / Hambley, T.W. / McAuley-Hecht, K. / Brown, T. / Hunter, W.N.
History
DepositionJan 21, 1993Deposition 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(*CP*GP*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,3382
Polymers1,8101
Non-polymers5281
Water88349
1
A: DNA (5'-D(*CP*GP*GP*CP*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)4,6754
Polymers3,6202
Non-polymers1,0552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)28.070, 28.070, 53.350
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*GP*CP*CP*G)-3')


Mass: 1810.205 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: pH 6.60, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE_HCL11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 277 K / pH: 6.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.3 mMhexanucleotide1drop
25.0 mManthracycline1drop
333 mMsodium cacodylate1drop
45.0 mM1dropMgCl2
52.0 mMspermine tetrahydrochloride1drop
68.3 %(v/v)1drop
7100 %MPD1reservoir

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. all: 3252 / Num. obs: 1742
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. all: 1742 / Num. obs: 1108 / Observed criterion σ(F): 2 / Num. measured all: 3252 / Rmerge(I) obs: 0.07

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.9→7 Å / σ(F): 2 /
RfactorNum. reflection
obs0.208 1108
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.9→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 38 49 207
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_it9.98
X-RAY DIFFRACTIONn_sugar_angle_it12.412
X-RAY DIFFRACTIONn_phos_bond_it12.612
X-RAY DIFFRACTIONn_phos_angle_it14.2412
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.0220.017
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.0540.03
X-RAY DIFFRACTIONn_phos_bond_d0.040.025
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0620.03
X-RAY DIFFRACTIONn_plane_restr0.0160.015
X-RAY DIFFRACTIONn_chiral_restr
X-RAY DIFFRACTIONn_singtor_nbd0.0690.063
X-RAY DIFFRACTIONn_multtor_nbd0.1350.063
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 7 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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