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- PDB-1d64: CRYSTAL STRUCTURE OF A PENTAMIDINE-OLIGONUCLEOTIDE COMPLEX: IMPLI... -

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Basic information

Entry
Database: PDB / ID: 1d64
TitleCRYSTAL STRUCTURE OF A PENTAMIDINE-OLIGONUCLEOTIDE COMPLEX: IMPLICATIONS FOR DNA-BINDING PROPERTIES
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homology1,5-BIS(4-AMIDINOPHENOXY)PENTANE / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsEdwards, K.J. / Jenkins, T.C. / Neidle, S.
CitationJournal: Biochemistry / Year: 1992
Title: Crystal structure of a pentamidine-oligonucleotide complex: implications for DNA-binding properties.
Authors: Edwards, K.J. / Jenkins, T.C. / Neidle, S.
History
DepositionMar 2, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 15, 1993Provider: 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_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

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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)7,6673
Polymers7,3272
Non-polymers3401
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.370, 40.000, 66.070
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-PNT / 1,5-BIS(4-AMIDINOPHENOXY)PENTANE


Mass: 340.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 289.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4NA CACODYLATE11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 289 K / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlDNA1drop
2100 mM1dropMgCl2
325 mMpentamidine1drop
450 %(v/v)MPD1drop
530 mMsodium cacodylate1drop
650 %(v/v)1reservoir

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.1 Å / Num. all: 10630 / Num. obs: 3824 / Rmerge(I) obs: 0.0699
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. all: 4256 / Num. measured all: 10630
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / Num. possible: 688 / Num. unique obs: 353

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.1→7 Å / σ(I): 2 /
RfactorNum. reflection
obs0.194 3113
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
ALL DRUG ATOMSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.1→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 25 77 588
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d
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_d0.017
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.03
X-RAY DIFFRACTIONn_phos_bond_d0.032
X-RAY DIFFRACTIONn_phos_bond_angle_d0.041
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: 2.1 Å / Lowest resolution: 7 Å / σ(I): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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