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- PDB-6w9p: Tel26 Parallel Four-quartet G-quadruplex with K+ -

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Basic information

Entry
Database: PDB / ID: 6w9p
TitleTel26 Parallel Four-quartet G-quadruplex with K+
ComponentsDNA (5'-D(P*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*T)-3')
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: 1.99 Å
AuthorsMcCarthy, S.E. / Yatsunyk, L.A. / Beseiso, D. / 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
DepositionMar 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 13, 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 18, 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

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Assembly

Deposited unit
A: DNA (5'-D(P*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4305
Polymers8,2891
Non-polymers1404
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, determined purity and homogeneity of the samples; the sample exist as a monomer, but on the gel three bands were obvious and the crystallized samples clearly ...Evidence: native gel electrophoresis, determined purity and homogeneity of the samples; the sample exist as a monomer, but on the gel three bands were obvious and the crystallized samples clearly represents only one of those bands. We have also conducted Circular Dichroism spectroscopy to obtaine conformation information - parallel vs antiparallel as well as CD thermal melting studies to obtain stability information.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.681, 38.681, 64.921
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: DNA chain DNA (5'-D(P*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*T)-3')


Mass: 8289.277 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DT26 has no base and only the phosphate is modeled.
Source: (synth.) Tetrahymena thermophila (eukaryote)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 1.73 Å3/Da / Density % sol: 29.1 %
Description: relatively think sheets, look clam-shell shaped.
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 32% PEG 2000, 0.3M sodium chloride, 0.05M sodium cacodylate pH 6.5
Temp details: Crystals grown at room temperature.

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Data collection

DiffractionMean temperature: 196 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 13, 2020
RadiationMonochromator: Cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.99→64.9 Å / Num. obs: 4116 / % possible obs: 99.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 45.95 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.1
Reflection shellResolution: 1.99→2.1 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.875 / Mean I/σ(I) obs: 1.6 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O0K

1o0k


Resolution: 1.99→33.5 Å / SU ML: 0.234 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.504
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.209 401 9.83 %random selection
Rwork0.197 ---
obs0.199 4078 98.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.94 Å2
Refinement stepCycle: LAST / Resolution: 1.99→33.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 551 4 30 585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005619
X-RAY DIFFRACTIONf_angle_d0.722961
X-RAY DIFFRACTIONf_dihedral_angle_d34.657256
X-RAY DIFFRACTIONf_chiral_restr0.036103
X-RAY DIFFRACTIONf_plane_restr0.00526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.280.33651340.27121175X-RAY DIFFRACTION97
2.28-2.870.30291250.26141213X-RAY DIFFRACTION100
2.87-33.50.17481420.16941289X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -10.6721 Å / Origin y: 6.7064 Å / Origin z: 6.0994 Å
111213212223313233
T0.2773 Å2-0.0386 Å2-0.029 Å2-0.2304 Å20.0086 Å2--0.3496 Å2
L4.7352 °2-0.1951 °2-1.0946 °2-3.9951 °20.9459 °2--4.2361 °2
S-0.1037 Å °0.0531 Å °0.065 Å °-0.2871 Å °-0.04 Å °-0.0467 Å °-0.482 Å °-0.0937 Å °0.1731 Å °
Refinement TLS groupSelection details: ALL

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