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- PDB-2dbe: CRYSTAL STRUCTURE OF A BERENIL-DODECANUCLEOTIDE COMPLEX: THE ROLE... -

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Basic information

Entry
Database: PDB / ID: 2dbe
TitleCRYSTAL STRUCTURE OF A BERENIL-DODECANUCLEOTIDE COMPLEX: THE ROLE OF WATER IN SEQUENCE-SPECIFIC LIGAND BINDING
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 / homologyBERENIL / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBrown, D.G. / Sanderson, M.R. / Skelly, J.V. / Jenkins, T.C. / Brown, T. / Garman, E. / Stuart, D.I. / Neidle, S.
CitationJournal: EMBO J. / Year: 1990
Title: Crystal structure of a berenil-dodecanucleotide complex: the role of water in sequence-specific ligand binding.
Authors: Brown, D.G. / Sanderson, M.R. / Skelly, J.V. / Jenkins, T.C. / Brown, T. / Garman, E. / Stuart, D.I. / Neidle, S.
History
DepositionMar 19, 1990Deposition site: BNL / Processing site: BNL
Revision 1.0Jul 15, 1991Provider: 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)7,6083
Polymers7,3272
Non-polymers2811
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.510, 39.980, 66.230
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-BRN / BERENIL / DIMINAZINE ACETURATE / 1,3-TRIS-(4'AMIDINOPHENYL)TRIAZINE


Mass: 281.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, temperature 278.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 278 K / pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mM1dropMgCl2
22 mMberenil1drop
320 %(v/v)MPD1drop
43 mMDNA dodecamer1drop
510 mMsodium cacodylate1drop
650 %(v/v)1reservoir

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: XENTRONICS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. all: 2195 / Num. obs: 1759 / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.037
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 2195 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.037 / Num. measured all: 5762

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Processing

Software
NameClassification
CORELSrefinement
NUCLSQrefinement
RefinementHighest resolution: 2.5 Å / σ(F): 2 /
RfactorNum. reflection
obs0.167 1759
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 21 48 555
Refinement
*PLUS
Highest resolution: 2.5 Å / σ(I): 2 / Rfactor obs: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32 Å2

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