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- PDB-1d30: THE STRUCTURE OF DAPI BOUND TO DNA -

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Basic information

Entry
Database: PDB / ID: 1d30
TitleTHE STRUCTURE OF DAPI BOUND TO DNA
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 / homology6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsLarsen, T. / Goodsell, D.S. / Cascio, D. / Grzeskowiak, K. / Dickerson, R.E.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 1989
Title: The structure of DAPI bound to DNA.
Authors: Larsen, T.A. / Goodsell, D.S. / Cascio, D. / Grzeskowiak, K. / Dickerson, R.E.
History
DepositionJan 4, 1991Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 15, 1992Provider: 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)7,6043
Polymers7,3272
Non-polymers2771
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.350, 40.710, 66.530
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-DAP / 6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE / DAPI


Mass: 277.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3SPERMINE11
4MG ACETATE11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.28 mMDNA1drop
20.22 mMspermine-HCl1drop
35.38 mMmagnesium acetate1drop
40.23 mM4'-6-diamidine-2-phenyl indole1drop
520 %(v/v)MPD1drop
640 %(v/v)1reservoir

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
DetectorType: SDMS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.4 Å / Num. all: 9292 / Num. obs: 2541
Reflection
*PLUS
Rmerge(I) obs: 0.116

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.4→10 Å / σ(F): 2 /
RfactorNum. reflection
obs0.222 2541
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 21 25 532
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 10 Å / Num. reflection all: 2541 / Num. reflection obs: 2428 / σ(F): 2 / Rfactor obs: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS

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