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- PDB-1eel: STRUCTURE OF A COMPLEX BETWEEN THE DNA SEQUENCE DCGCGAATTCGCG AND... -

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Basic information

Entry
Database: PDB / ID: 1eel
TitleSTRUCTURE OF A COMPLEX BETWEEN THE DNA SEQUENCE DCGCGAATTCGCG AND BIS[PIPERIDINO-ETHYL]-FURAMIDINE
Components5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
KeywordsDNA / MINOR GROOVE BINDING LIGAND / B-DNA / BULKY SIDE-CHAINS
Function / homologyChem-D24 / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNeidle, S. / Simpson, I.J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: A thermodynamic and structural analysis of DNA minor-groove complex formation.
Authors: Mazur, S. / Tanious, F.A. / Ding, D. / Kumar, A. / Boykin, D.W. / Simpson, I.J. / Neidle, S. / Wilson, W.D.
History
DepositionFeb 1, 2000Deposition site: NDB / Processing site: RCSB
Revision 1.0Feb 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
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_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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,7633
Polymers7,3272
Non-polymers4371
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.7, 40.73, 66.38
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-D24 / 2,5-BIS-[4-[CYCLOPENTA-1,3-DIEN-5-YLAMINO-1-AMINOMETHYL]-PHEN-1-YL]FURAN


Mass: 436.548 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H28N4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD 3 UL OF 25%, MGCL2 2UL OF 90MM, SPERMINE 1UL OF 10MM, DNA 2UL OF 2MM, LIGAND 2UL OF 3MM, MPD IN RESERVOIR 1ML OF 30%, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MGCL211
2SPERMINE11
3MPD11
4MPD12
Crystal grow
*PLUS
Temperature: 286 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
190 mM1dropMgCl2
210 mMspermine1drop
32 mMDNA1drop
43 mMdrug1drop
525 %(v/v)MPD1drop
630 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 20, 1998 / Details: YALE FOCUSSING MIRRORS
RadiationMonochromator: Y / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→12 Å / Num. obs: 3105 / % possible obs: 94.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 9.6
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 12 Å / Num. all: 3292 / Num. measured all: 18138

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DNA PART OF NDB STRUCTURE GDL044

Resolution: 2.4→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: PARKINSON ET AL. / Details: USED SHELX-97 PROCEDURE
RfactorNum. reflectionSelection details
Rfree0.227 -RANDOM
obs0.184 --
all-3105 -
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 33 91 610
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.012
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Rfactor all: 0.184 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS

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