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- PDB-130d: MOLECULAR STRUCTURE OF D(CGC[E6G]AATTCGCG) COMPLEXED WITH HOECHST... -

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Basic information

Entry
Database: PDB / ID: 130d
TitleMOLECULAR STRUCTURE OF D(CGC[E6G]AATTCGCG) COMPLEXED WITH HOECHST 33342
ComponentsDNA (5'-D(*CP*GP*CP*(G36)P*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED
Function / homologyChem-HT1 / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsSriram, M. / Van Der Marel, G.A. / Roelen, H.L.P.F. / Van Boom, J.H. / Wang, A.H.-J.
CitationJournal: EMBO J. / Year: 1992
Title: Conformation of B-DNA containing O6-ethyl-G-C base pairs stabilized by minor groove binding drugs: molecular structure of d(CGC[e6G]AATTCGCG complexed with Hoechst 33258 or Hoechst 33342.
Authors: Sriram, M. / van der Marel, G.A. / Roelen, H.L. / van Boom, J.H. / Wang, A.H.
History
DepositionJun 30, 1993Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 15, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 24, 2011Group: Atomic model
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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*CP*(G36)P*AP*AP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*(G36)P*AP*AP*TP*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8353
Polymers7,3832
Non-polymers4531
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.710, 41.320, 67.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*CP*GP*CP*(G36)P*AP*AP*TP*TP*CP*GP*CP*G)-3')


Mass: 3691.445 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-HT1 / 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE / HOECHST 33342


Mass: 452.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H28N6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
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
4MGCL211
5SPERMINE11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.8 mMdodecamer1dropsingle strand concentration
231 mMcacodylate1drop
34 mM1dropMgCl2
41 mMspermine1drop
50.8 mMdrug1drop
62 %MPD1drop
750 %1reservoir

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 1194 / Observed criterion σ(F): 2

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementHighest resolution: 2.5 Å / σ(F): 2 /
RfactorNum. reflection
obs0.157 1194
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 490 34 68 592
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.02
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_d
X-RAY DIFFRACTIONn_sugar_bond_angle_d
X-RAY DIFFRACTIONn_phos_bond_d
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: 2.5 Å / Num. reflection obs: 1194 / Rfactor obs: 0.157 / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: n_bond_d / Dev ideal: 0.019

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