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- PDB-3l1q: The crystal structure of the undecamer d(TGGCCTTAAGG) -

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Basic information

Entry
Database: PDB / ID: 3l1q
TitleThe crystal structure of the undecamer d(TGGCCTTAAGG)
Components5'-D(*TP*GP*GP*CP*CP*TP*TP*AP*AP*GP*G)-3'
KeywordsDNA / triple helix / triplet / Hoogsteen / reverse-Hoogsteen
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVan Hecke, K.
CitationJournal: Cryst.Growth Des. / Year: 2010
Title: Designing Triple Helical Fragments: The Crystal Structure of the Undecamer d(TGGCCTTAAGG) Mimicking T·AT Base Triplets
Authors: Van Hecke, K. / Uytterhoeven, K. / Voet, A. / De Maeyer, M. / Van Meervelt, L.
History
DepositionDec 14, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionOct 27, 2010ID: 1K71
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,7782
Polymers6,7782
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-5 kcal/mol
Surface area4710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.050, 41.070, 52.570
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 5'-D(*TP*GP*GP*CP*CP*TP*TP*AP*AP*GP*G)-3'


Mass: 3389.221 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: THE OLIGONUCLEOTIDE WAS PURCHASED FROM OSWEL DNA SERVICE (UNIVERSITY OF SOUTHAMPTON, UK)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 21.1mM sodium cacodylate, 47.4mM magnesium chloride, 21.1% MPD, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.2 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 4, 2001
RadiationMonochromator: Si 111 horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.5→32.4 Å / Num. obs: 2203 / % possible obs: 98.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 86.8 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 14.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 1.8 / Num. unique all: 307 / % possible all: 98.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 431D

431d


Resolution: 2.5→20.76 Å / Cor.coef. Fo:Fc: 0.955 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.492 / SU ML: 0.171 / Isotropic thermal model: isotropic / σ(F): 0 / ESU R: 0.851 / Stereochemistry target values: Engh & Huber
Details: MAXIMUM LIKELIHOOD; in the final refinement cycles of the structure, no Rfree was used. Please see the details in the primary citation.
RfactorNum. reflection% reflectionSelection details
Rwork0.22325 ---
obs0.22325 2192 97.73 %-
all-2192 --
Rfree---RANDOM
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 86.26 Å2 / Biso mean: 50.199 Å2 / Biso min: 28.89 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å20 Å20 Å2
2--8.07 Å20 Å2
3----6.35 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 450 0 44 494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021508
X-RAY DIFFRACTIONr_angle_refined_deg2.8183776
X-RAY DIFFRACTIONr_chiral_restr0.1110.286
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02236
X-RAY DIFFRACTIONr_scbond_it2.3373458
X-RAY DIFFRACTIONr_scangle_it3.5594.5705
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.407 162 -
Rfree-0 -
obs-162 99.39 %

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