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- PDB-4dnb: METHYLATION OF THE ECORI RECOGNITION SITE DOES NOT ALTER DNA CONF... -

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Basic information

Entry
Database: PDB / ID: 4dnb
TitleMETHYLATION OF THE ECORI RECOGNITION SITE DOES NOT ALTER DNA CONFORMATION. THE CRYSTAL STRUCTURE OF D(CGCGAM6ATTCGCG) AT 2.0 ANGSTROMS RESOLUTION
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*(6MA)P*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsFrederick, C.A. / Quigley, G.J. / Van Der Marel, G.A. / Van Boom, J.H. / Wang, A.H.-J. / Rich, A.
CitationJournal: J.Biol.Chem. / Year: 1988
Title: Methylation of the EcoRI recognition site does not alter DNA conformation: the crystal structure of d(CGCGAm6ATTCGCG) at 2.0-A resolution.
Authors: Frederick, C.A. / Quigley, G.J. / van der Marel, G.A. / van Boom, J.H. / Wang, A.H. / Rich, A.
History
DepositionAug 29, 1988Deposition site: BNL / Processing site: BNL
Revision 1.0Jan 9, 1989Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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*(6MA)P*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*(6MA)P*TP*TP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3552
Polymers7,3552
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.620, 40.390, 67.320
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*(6MA)P*TP*TP*CP*GP*CP*G)-3')


Mass: 3677.418 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4NA CACODYLATE11
5SPERMINE11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.2 mMd(CGCGAm6ATTCGCG)1dropsingle strand
21.5 mM1dropMgCl2
320 mMsodium cacodylate1drop
43 mMspermine tetrachloride1drop
510 %MPD1drop
61
71

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Data collection

DiffractionMean temperature: 288 K
DetectorType: NICOLET / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2 Å / Num. obs: 2379 / Observed criterion σ(F): 2
Reflection
*PLUS
% possible obs: 55 %

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementHighest resolution: 2 Å / σ(F): 2 /
RfactorNum. reflection
obs0.169 2379
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 2 87 575
Refinement
*PLUS
Highest resolution: 2 Å / Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS

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