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- PDB-7ll0: Crystal structure of a four-tetrad, parallel, and K+ stabilized T... -

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Basic information

Entry
Database: PDB / ID: 7ll0
TitleCrystal structure of a four-tetrad, parallel, and K+ stabilized Tetrahymena thermophila telomeric G-quadruplex
Components26-mer DNA
KeywordsDNA / G-quadruplex / Parallel / Four-quartets / propeller loops
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYatsunyk, L.A. / Chen, E.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R15CA253134 United States
Other privateDreyfus Teacher-Scholar United States
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: The first crystal structures of hybrid and parallel four-tetrad intramolecular G-quadruplexes.
Authors: Beseiso, D. / Chen, E.V. / McCarthy, S.E. / Martin, K.N. / Gallagher, E.P. / Miao, J. / Yatsunyk, L.A.
History
DepositionFeb 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 26-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4465
Polymers8,2891
Non-polymers1564
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, Native PAGE showed the presence of two conformations of seemingly monomeric GQs for this sequence.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.090, 36.474, 53.253
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-101-

K

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Components

#1: DNA chain 26-mer DNA


Mass: 8289.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Tetrahymena thermophila (eukaryote)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.81 Å3/Da / Density % sol: 32 % / Description: Irregular clamshell shaped crystals.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: sodium cacodylate, KCl, PEG, NaCl, ethylene glycol

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Data collection

DiffractionMean temperature: 196 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.99→53.25 Å / Num. obs: 4313 / % possible obs: 99.6 % / Redundancy: 8.9 % / Biso Wilson estimate: 63.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.025 / Rrim(I) all: 0.074 / Net I/σ(I): 12
Reflection shellResolution: 1.99→2.05 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 299 / CC1/2: 0.418 / Rpim(I) all: 0.753 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PHENIX1.18_3845phasing
XDSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JKU

7jku


Resolution: 2→30.09 Å / SU ML: 0.352 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 44.2386
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2392 413 10.08 %
Rwork0.2143 3683 -
obs0.2168 4096 95.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.11 Å2
Refinement stepCycle: LAST / Resolution: 2→30.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 523 4 5 532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097587
X-RAY DIFFRACTIONf_angle_d1.0449910
X-RAY DIFFRACTIONf_chiral_restr0.049199
X-RAY DIFFRACTIONf_plane_restr0.008324
X-RAY DIFFRACTIONf_dihedral_angle_d37.0127246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.280.42711330.38611191X-RAY DIFFRACTION94.84
2.28-2.880.29261330.3121192X-RAY DIFFRACTION94.51
2.88-30.090.21791470.18471300X-RAY DIFFRACTION95.95
Refinement TLS params.Method: refined / Origin x: -2.97017377611 Å / Origin y: -13.9998889043 Å / Origin z: 6.20978816577 Å
111213212223313233
T0.45992453339 Å2-0.026133124011 Å20.0873056941154 Å2-0.401686389489 Å2-0.0665523005293 Å2--0.351991698692 Å2
L11.2608202925 °21.87694358529 °2-2.94980326917 °2-12.1718669174 °21.05022531307 °2--10.1562233511 °2
S0.254776991007 Å °-0.535271416869 Å °0.33809239362 Å °1.00066973762 Å °-0.177973381181 Å °0.448804992128 Å °-0.752274322775 Å °-0.295049923887 Å °-0.0472778718175 Å °
Refinement TLS groupSelection details: all

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