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- PDB-154d: DNA DISTORTION IN BIS-INTERCALATED COMPLEXES -

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Basic information

Entry
Database: PDB / ID: 154d
TitleDNA DISTORTION IN BIS-INTERCALATED COMPLEXES
ComponentsDNA (5'-D(*(CBR)P*GP*CP*G)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED
Function / homologyChem-FLD / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsPeek, M.E. / Lipscomb, L.A. / Bertrand, J.A. / Gao, Q. / Roques, B.P. / Garbay-Jaureguiberry, C. / Williams, L.D.
CitationJournal: Biochemistry / Year: 1994
Title: DNA distortion in bis-intercalated complexes.
Authors: Peek, M.E. / Lipscomb, L.A. / Bertrand, J.A. / Gao, Q. / Roques, B.P. / Garbay-Jaureguiberry, C. / Williams, L.D.
History
DepositionDec 14, 1993Deposition site: BNL / Processing site: NDB
Revision 1.0Aug 31, 1994Provider: 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_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(*(CBR)P*GP*CP*G)-3')
B: DNA (5'-D(*(CBR)P*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,2103
Polymers2,5412
Non-polymers6691
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.090, 27.090, 81.890
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(*(CBR)P*GP*CP*G)-3')


Mass: 1270.714 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-FLD / BIS-(N-ETHYLPYRIDINIUM-(3-METHOXYCARBAZOLE))HEXANE-1,6-DIAMINE / FLEXI-DI


Mass: 668.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H48N6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.96 Å3/Da / Density % sol: 58.39 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5WATER12
6MPD12
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
118 mMsodium cacodylate1drop
20.7 mMDNA1dropsingle strand concentration
30.2 mMFlexi Di1drop
43.9 mM1dropMgCl2
53.1 %MPD1drop
610 %1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: SDMS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. all: 2139 / Num. obs: 1183 / Observed criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 2.5 Å / % possible obs: 98 % / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.0663

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Processing

Software
NameVersionClassification
PROLSQ(MODIFIED BY G.J.QUIGLEY)refinement
MODIFIEDBY G.J.QUIGLEYrefinement
RefinementResolution: 2.5→7.1 Å / σ(F): 2 /
RfactorNum. reflection% reflection
obs0.239 1183 99.7 %
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.5→7.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 158 52 27 237
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.021
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 7.1 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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