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- PDB-198d: A TRIGONAL FORM OF THE IDARUBICIN-D(CGATCG) COMPLEX: CRYSTAL AND ... -

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Basic information

Entry
Database: PDB / ID: 198d
TitleA TRIGONAL FORM OF THE IDARUBICIN-D(CGATCG) COMPLEX: CRYSTAL AND MOLECULAR STRUCTURE AT 2.0 ANGSTROMS RESOLUTION
ComponentsDNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homologyIDARUBICIN / SPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.97 Å
AuthorsDautant, A. / Langlois D'Estaintot, B. / Gallois, B. / Brown, T. / Hunter, W.N.
Citation
Journal: Nucleic Acids Res. / Year: 1995
Title: A trigonal form of the idarubicin:d(CGATCG) complex; crystal and molecular structure at 2.0 A resolution.
Authors: Dautant, A. / Langlois d'Estaintot, B. / Gallois, B. / Brown, T. / Hunter, W.N.
#1: Journal: Anti-Cancer Drug Des. / Year: 1991
Title: Influence of Aglycone Modifications on the Binding of Anthracycline Drugs to DNA: The Molecular Structure of Idarubicin and 4-O-Demethyl-11-Deoxydoxorubicin Complexed to d(CGATCG)
Authors: Gao, Y.-G. / Wang, A.H.-J.
History
DepositionNov 28, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Mar 15, 1995Provider: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)9,4299
Polymers7,2374
Non-polymers2,1925
Water2,882160
1
A: DNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
B: DNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8165
Polymers3,6182
Non-polymers1,1973
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
D: DNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,6134
Polymers3,6182
Non-polymers9952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.996, 52.996, 33.065
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 1809.217 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Chemical
ChemComp-DM5 / IDARUBICIN / 4-DEMETHOXY-DAUNORUBICIN


Mass: 497.494 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H27NO9
#3: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.7 Å3/Da / Density % sol: 66.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4NA CACODYLATE11
5SPERMINE_HCL11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 277 K / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.4 mMoligonucleotide1dropsingle strand concentration
22 mMidarubicin1drop
3136 mM1dropMgCl2
427 mMsodium cacodylate1drop
54 mMspermine tetrachloride1drop
69 %(v/v)MPD1drop
750 %1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU AFC-5 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2 Å / Num. all: 7276 / Observed criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. obs: 3768 / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.061

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.97→18 Å / σ(F): 2 /
RfactorNum. reflection
obs0.188 3768
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.97→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 480 158 160 798
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_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_d0.0250.025
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.040.04
X-RAY DIFFRACTIONn_phos_bond_d0.0680.035
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0370.045
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
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.068
X-RAY DIFFRACTIONx_angle_d0.037
X-RAY DIFFRACTIONx_planar_d
X-RAY DIFFRACTIONx_plane_restr
X-RAY DIFFRACTIONx_chiral_restr

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