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- PDB-1ftd: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'-SYMMETRIC BIS-BENZIM... -

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Basic information

Entry
Database: PDB / ID: 1ftd
Title5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'-SYMMETRIC BIS-BENZIMIDAZOLE COMPLEX
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / MINOR GROOVE BINDING
Function / homologyChem-E97 / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsMann, J. / Baron, A. / Opoku-Boahen, Y. / Johansson, E. / Parkinson, G. / Kelland, L.R. / Neidle, S.
CitationJournal: J.Med.Chem. / Year: 2001
Title: A new class of symmetric bisbenzimidazole-based DNA minor groove-binding agents showing antitumor activity.
Authors: Mann, J. / Baron, A. / Opoku-Boahen, Y. / Johansson, E. / Parkinson, G. / Kelland, L.R. / Neidle, S.
History
DepositionSep 12, 2000Deposition site: NDB / Processing site: NDB
Revision 1.0Feb 26, 2001Provider: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9404
Polymers7,3272
Non-polymers6132
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.15, 39.94, 65.65
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*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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-E97 / [3-(4-{2'-[4-(3-DIMETHYLAMINO-PROPOXY)-PHENYL]-3H,3'H-[5,5']BIBENZOIMIDAZOLYL-2-YL}-PHENOXY)-PROPYL]-DIMETHYL-AMINE


Mass: 588.742 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H40N6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 284 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: SODIUM CACODYLATE, MPD, SPERMINE TETRAHYDROCHLORIDE, NACL, MGCL2, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 284K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2SPERMINE TETRAHYDROCHLORIDE11
3NACL11
4MGCL211
5MPD11
6MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11 mMDNA1dropsingle stranded
210 mMsodium cacodylate1drop
30.5 mMcompound 51drop
45 %MPD1drop
56 mMspermine tetrahydrochloride1drop
640 mM1dropNaCl
710 mM1MgCl2
835 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 4891 / Num. obs: 4427 / % possible obs: 92.9 % / Observed criterion σ(I): 3 / Redundancy: 1.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 27.9
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.1

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2→8 Å / σ(F): 4
RfactorNum. reflectionSelection details
Rfree0.292 448 RANDOM 10%
Rwork0.244 --
all0.249 4198 -
obs0.242 4063 -
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 51 79 616
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 4 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_mcbond_it
X-RAY DIFFRACTIONs_scbond_it
X-RAY DIFFRACTIONs_mcangle_it
X-RAY DIFFRACTIONs_scangle_it

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