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

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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
MethodX-RAY DIFFRACTION / 1.8 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 10, 1994 / Release: Jul 10, 1995
RevisionDateData content typeGroupProviderType
1.0Jul 10, 1995Structure modelrepositoryInitial release
1.1May 22, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
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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
Polyers2,1131
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
Polyers4,2272
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Unit cell
γ
α
β
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-MC 2 2 2

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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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Formula: H2O / Water

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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 / Density percent 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
Temp: 18-22 ℃ / pH: 6.8
Crystal grow comp
*PLUS
IDConcCommon 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 kelvins
DetectorType: SYNTEX P21 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
D resolution high: 1.8 Å / Number obs: 1606 / Number measured all: 4259 / Rmerge I obs: 0.025

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Processing

Software
NameClassification
X-PLORrefinement
NUCLSQrefinement
RefineSigma F: 0
Least-squares processR factor R work: 0.214 / R factor obs: 0.214 / Highest resolution: 1.8 Å / Lowest resolution: 7 Å / Number reflection obs: 1579 / Percent reflection obs: 96
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 7 Å
Number of atoms included #LASTProtein: 0 / Nucleic acid: 140 / Ligand: 2 / Solvent: 48 / Total: 190
Refine
*PLUS
Sigma F: 0
Least-squares process
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 7 Å
Refine LS restraints
*PLUS
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_plane_restr0.0150030
X-RAY DIFFRACTIONx_chiral_restr0.285

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