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- PDB-200d: STABLE LOOP IN THE CRYSTAL STRUCTURE OF THE INTERCALATED FOUR-STR... -

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Basic information

Entry
Database: PDB / ID: 200d
TitleSTABLE LOOP IN THE CRYSTAL STRUCTURE OF THE INTERCALATED FOUR-STRANDED CYTOSINE-RICH METAZOAN TELOMERE
ComponentsDNA (5'-D(*TP*AP*AP*CP*CP*C)-3')
KeywordsDNA / U-DNA / QUADRUPLE HELIX / TETRAPLEX / BASE INTERCALATED / LOOP
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsKang, C. / Berger, I. / Lockshin, C. / Ratliff, R. / Moyzis, R. / Rich, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Stable loop in the crystal structure of the intercalated four-stranded cytosine-rich metazoan telomere.
Authors: Kang, C. / Berger, I. / Lockshin, C. / Ratliff, R. / Moyzis, R. / Rich, A.
History
DepositionFeb 16, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 31, 1995Provider: 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*TP*AP*AP*CP*CP*C)-3')
B: DNA (5'-D(*TP*AP*AP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)3,5062
Polymers3,5062
Non-polymers00
Water46826
1
A: DNA (5'-D(*TP*AP*AP*CP*CP*C)-3')
B: DNA (5'-D(*TP*AP*AP*CP*CP*C)-3')

A: DNA (5'-D(*TP*AP*AP*CP*CP*C)-3')
B: DNA (5'-D(*TP*AP*AP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,0134
Polymers7,0134
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)59.940, 81.330, 26.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: DNA chain DNA (5'-D(*TP*AP*AP*CP*CP*C)-3')


Mass: 1753.194 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growMethod: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE11
5KCL11
6K CACODYLATE11
7WATER12
8MPD12
Crystal grow
*PLUS
pH: 6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formula
15 %(v/v)MPD1
220 mM1MgCl2
30.10 mMspermine1
480 mM1KCl
540 mMpotassium cacodylate1
62 mMDNA1
735 %MPD1
81

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 20, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionRmerge(I) obs: 0.045
Reflection
*PLUS
% possible obs: 77 %

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Processing

Software
NameClassification
X-PLORrefinement
MSCdata reduction
RefinementResolution: 1.85→12 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.223 --
Rwork0.19 --
obs0.19 2122 77 %
Refinement stepCycle: LAST / Resolution: 1.85→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 258 0 26 284
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.03
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 12 Å / σ(F): 1 / Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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