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- PDB-1d14: STRUCTURE OF 11-DEOXYDAUNOMYCIN BOUND TO DNA CONTAINING A PHOSPHO... -

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Basic information

Entry
Database: PDB / ID: 1d14
TitleSTRUCTURE OF 11-DEOXYDAUNOMYCIN BOUND TO DNA CONTAINING A PHOSPHOROTHIOATE
ComponentsDNA (5'-D(*CP*GP*TP*(AS)P*CP*G)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED
Function / homology6-DEOXYDAUNOMYCIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsWilliams, L.D. / Egli, M. / Ughetto, G. / Van Der Marel, G.A. / Van Boom, J.H. / Quigley, G.J. / Wang, A.H.-J. / Rich, A. / Frederick, C.A.
CitationJournal: J.Mol.Biol. / Year: 1990
Title: Structure of 11-deoxydaunomycin bound to DNA containing a phosphorothioate.
Authors: Williams, L.D. / Egli, M. / Ughetto, G. / van der Marel, G.A. / van Boom, J.H. / Quigley, G.J. / Wang, A.H. / Rich, A. / Frederick, C.A.
History
DepositionOct 20, 1989Deposition site: BNL / Processing site: BNL
Revision 1.0Oct 15, 1990Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 7, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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*TP*(AS)P*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,3372
Polymers1,8251
Non-polymers5121
Water66737
1
A: DNA (5'-D(*CP*GP*TP*(AS)P*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)4,6744
Polymers3,6512
Non-polymers1,0232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Unit cell
Length a, b, c (Å)17.730, 19.130, 26.360
Angle α, β, γ (deg.)90.00, 98.01, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-44-

HOH

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Components

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


Mass: 1825.282 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-DM3 / 6-DEOXYDAUNOMYCIN


Mass: 511.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29NO9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.43 Å3/Da / Density % sol: 49.28 %
Crystal growMethod: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4SPERMINE11
5MGCL211
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.5 mMDNA1dropsingle strand
220 mMsodium cacodylate1drop
36.0 mM1dropMgCl2
41.5 mMspermine1drop
520 %MPD1drop
630 %MPD1reservoir
71

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Data collection

DiffractionMean temperature: 283 K
DetectorType: NICOLET P3 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.5 Å / Num. obs: 2129 / Observed criterion σ(F): 2

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementHighest resolution: 1.5 Å / σ(F): 2 /
RfactorNum. reflection
obs0.224 2129
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Highest resolution: 1.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 119 38 37 194
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.7 Å / Num. reflection obs: 2129 / σ(F): 2 / Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: n_bond_d / Dev ideal: 0.038

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