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- PDB-184d: SELF-ASSOCIATION OF A DNA LOOP CREATES A QUADRUPLEX: CRYSTAL STRU... -

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Basic information

Entry
Database: PDB / ID: 184d
TitleSELF-ASSOCIATION OF A DNA LOOP CREATES A QUADRUPLEX: CRYSTAL STRUCTURE OF D(GCATGCT) AT 1.8 ANGSTROMS RESOLUTION
ComponentsDNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
KeywordsDNA / U-DNA / QUADRUPLE HELIX / TETRAPLEX / LOOP
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsLeonard, G.A. / Zhang, S. / Peterson, M.R. / Harrop, S.J. / Helliwell, J.R. / Cruse, W.B.T. / Langlois D'Estaintot, B. / Kennard, O. / Brown, T. / Hunter, W.N.
CitationJournal: Structure / Year: 1995
Title: Self-association of a DNA loop creates a quadruplex: crystal structure of d(GCATGCT) at 1.8 A resolution.
Authors: Leonard, G.A. / Zhang, S. / Peterson, M.R. / Harrop, S.J. / Helliwell, J.R. / Cruse, W.B. / d'Estaintot, B.L. / Kennard, O. / Brown, T. / Hunter, W.N.
History
DepositionAug 10, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 10, 1995Provider: 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

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,1623
Polymers2,1131
Non-polymers492
Water86548
1
A: DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
hetero molecules

A: DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3246
Polymers4,2272
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)22.520, 59.370, 24.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-8-

MG

21A-9-

MG

31A-10-

HOH

41A-11-

HOH

51A-12-

HOH

61A-13-

HOH

71A-14-

HOH

81A-52-

HOH

91A-54-

HOH

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Components

#1: DNA chain DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')


Mass: 2113.410 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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: 1.93 Å3/Da / Density % sol: 36.12 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.8 / Details: pH 6.80, VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2HEXANE-1,6-DIOL11
3LI CACODYLATE11
4MGCL211
5SPERMINE_HCL11
6WATER12
7HEXANE-1,6-DIOL12
Crystal grow
*PLUS
Temperature: 18-22 ℃ / pH: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlheptanucleotide1drop
250 mMlithium cacodylate1drop
350 mMmagnesium chloride1drop
43 mMspermine tetrahydrochloride1drop
510 %(v/v)hexane-1,6-diol1drop
650 %(v/v)hexane-1,6-diol1reservoir
71

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Data collection

DiffractionMean temperature: 279 K
DetectorType: SYNTEX P21 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 1606 / Num. measured all: 4259 / Rmerge(I) obs: 0.025

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Processing

Software
NameClassification
X-PLORrefinement
NUCLSQrefinement
RefinementResolution: 1.8→7 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.214 --
obs0.214 1579 96 %
Refinement stepCycle: LAST / Resolution: 1.8→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 140 2 48 190
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 7 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_plane_restr0.01530
X-RAY DIFFRACTIONx_chiral_restr0.285

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