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

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Basic information

Entry
Database: PDB / ID: 7jku
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: 1.97 Å
AuthorsYatsunyk, L.A. / McCarthy, S.E. / Beseiso, D. / Gallagher, E.P. / Chen, E.V. / Miao, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R15CA208676-01A1 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
DepositionJul 28, 2020Deposition 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 1.2Apr 3, 2024Group: 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

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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
Water1629
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)32.042, 39.110, 59.020
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 / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.29 Å3/Da / Density % sol: 46.2 %
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: May 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.97→59.02 Å / Num. obs: 5471 / % possible obs: 97.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 56.93 Å2 / CC1/2: 0.994 / Net I/σ(I): 7.7
Reflection shellResolution: 1.97→2.02 Å / Num. unique obs: 381 / CC1/2: 0.343

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
Cootmodel building
XDSdata scaling
PHENIX1.18.2_3874phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TEL26-1

Resolution: 1.97→32.6 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 46.9033
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2615 525 9.93 %
Rwork0.2467 4760 -
obs0.2484 5285 94.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.16 Å2
Refinement stepCycle: LAST / Resolution: 1.97→32.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 524 4 9 537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062589
X-RAY DIFFRACTIONf_angle_d0.7559913
X-RAY DIFFRACTIONf_chiral_restr0.0378100
X-RAY DIFFRACTIONf_plane_restr0.004223
X-RAY DIFFRACTIONf_dihedral_angle_d36.7653253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.170.45811170.42541049X-RAY DIFFRACTION85.48
2.17-2.480.32711340.31311202X-RAY DIFFRACTION97.31
2.48-3.130.30641320.31991216X-RAY DIFFRACTION97.12
3.13-32.60.23331420.21261293X-RAY DIFFRACTION97.03
Refinement TLS params.Method: refined / Origin x: -4.14107878033 Å / Origin y: -16.0483557086 Å / Origin z: 6.63266892569 Å
111213212223313233
T0.466441720072 Å2-0.0219530367008 Å20.0318883642678 Å2-0.351739657003 Å2-0.0283544336139 Å2--0.460411686442 Å2
L7.24008320119 °20.291921999987 °20.955635605828 °2-5.37570556772 °2-0.909194399676 °2--7.15479469542 °2
S-0.0514612234559 Å °-0.515576951101 Å °0.531256548316 Å °0.574795317662 Å °0.104451761227 Å °-0.00802804428397 Å °-0.124814034655 Å °0.128033781789 Å °-0.0690939329881 Å °
Refinement TLS groupSelection details: all

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