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- PDB-1d67: THE MOLECULAR STRUCTURE OF AN IDARUBICIN-D(TGATCA) COMPLEX AT HIG... -

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Basic information

Entry
Database: PDB / ID: 1d67
TitleTHE MOLECULAR STRUCTURE OF AN IDARUBICIN-D(TGATCA) COMPLEX AT HIGH RESOLUTION
ComponentsDNA (5'-D(*TP*GP*AP*TP*CP*A)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homologyIDARUBICIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsGallois, B. / Langlois D'Estaintot, B. / Brown, T. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1993
Title: The structure of an idarubicin-d(TGATCA) complex at high resolution.
Authors: Gallois, B. / d'Estaintot, B.L. / Brown, T. / Hunter, W.N.
History
DepositionMar 31, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 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*AP*TP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,3062
Polymers1,8081
Non-polymers4971
Water63135
1
A: DNA (5'-D(*TP*GP*AP*TP*CP*A)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)4,6114
Polymers3,6162
Non-polymers9952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)28.190, 28.190, 52.770
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*AP*TP*CP*A)-3')


Mass: 1808.229 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-DM5 / IDARUBICIN / 4-DEMETHOXY-DAUNORUBICIN


Mass: 497.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H27NO9
#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

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, temperature 295.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MG ACETATE11
5SPERMINE_HCL11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 295 K / pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11 mMd(TGATCA)1drop
21.2 mMidarubicin1drop
350 mMsodium cacodylate1drop
4100 mMmagnesium acetate1drop
50.5 mMspermine hydrochloride1drop
610 %MPD1drop
750 %1reservoiraqueous

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU AFC-5 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.5 Å / Num. obs: 4578
Reflection
*PLUS
Highest resolution: 1.5 Å

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.6→8 Å / σ(F): 3 /
RfactorNum. reflection
obs0.222 2032
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 36 35 191
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_d0.02
X-RAY DIFFRACTIONn_sugar_bond_angle_d
X-RAY DIFFRACTIONn_phos_bond_d0.03
X-RAY DIFFRACTIONn_phos_bond_angle_d
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: 1.6 Å / Lowest resolution: 8 Å / Num. reflection obs: 2032 / σ(F): 3 / Rfactor obs: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONn_bond_d0.02
X-RAY DIFFRACTIONn_angle_d0.040.05
X-RAY DIFFRACTIONn_plane_restr0.020.02
X-RAY DIFFRACTIONn_mcbond_it64.44
X-RAY DIFFRACTIONn_mcangle_it64.96

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