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- PDB-1ley: STRUCTURE OF A DICATIONIC MONOIMIDAZOLE LEXITROPSIN BOUND TO DNA ... -

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Basic information

Entry
Database: PDB / ID: 1ley
TitleSTRUCTURE OF A DICATIONIC MONOIMIDAZOLE LEXITROPSIN BOUND TO DNA (ORIENTATION 2)
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 / homologyMONOIMIDAZOLE LEXITROPSIN / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsGoodsell, D.S. / Ng, H.L. / Kopka, M.L. / Lown, J.W. / Dickerson, R.E.
CitationJournal: Biochemistry / Year: 1995
Title: Structure of a dicationic monoimidazole lexitropsin bound to DNA.
Authors: Goodsell, D.S. / Ng, H.L. / Kopka, M.L. / Lown, J.W. / Dickerson, R.E.
History
DepositionOct 10, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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)7,7583
Polymers7,3272
Non-polymers4311
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.030, 39.260, 66.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 DNA CHAINS AND 1 MONOIMIDAZOLE LEXITROPSIN MOLECULE. INDEPENDENT REFINEMENTS OF THE STRUCTURE WERE CARRIED OUT WITH THE LEXITROPSIN MOLECULE IN TWO DIFFERENT ORIENTATIONS. IT COULD NOT BE DETERMINED WHICH OF THESE ORIENTATIONS WAS CORRECT. THE TWO SETS OF COORDINATES ARE AVAILABLE IN THE PDB FILES 1LEX AND 1LEY.

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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-ILT / MONOIMIDAZOLE LEXITROPSIN


Mass: 431.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H25N11O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.04 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 278.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MG ACETATE11
4SPERMINE_HCL11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 5 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.43 mMDNA duplex1drop
26.0 mMmagnesium acetate1drop
30.2 mMspermine hydrochloride1drop
40.73 mMdrug1drop
58.8 %(w/v)MPD1drop
640 %(w/v)1reservoir

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Data collection

DiffractionMean temperature: 248 K
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.25 Å

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.25→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.235 --
obs0.164 2322 86 %
Refinement stepCycle: LAST / Resolution: 2.25→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 31 37 554
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_it5.486
X-RAY DIFFRACTIONn_sugar_angle_it6.2666
X-RAY DIFFRACTIONn_phos_bond_it5.3436
X-RAY DIFFRACTIONn_phos_angle_it5.8436
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.0250.03
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.0490.04
X-RAY DIFFRACTIONn_phos_bond_d0.030.025
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0690.05
X-RAY DIFFRACTIONn_plane_restr0.0150.02
X-RAY DIFFRACTIONn_chiral_restr0.1440.15
X-RAY DIFFRACTIONn_singtor_nbd0.1070.1
X-RAY DIFFRACTIONn_multtor_nbd0.0930.1
X-RAY DIFFRACTIONn_xhyhbond_nbd

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