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- PDB-8d79: Crystal structure of a four-tetrad, parallel, and Na+ stabilized ... -

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Basic information

Entry
Database: PDB / ID: 8d79
TitleCrystal structure of a four-tetrad, parallel, and Na+ stabilized Tetrahymena thermophila telomeric G-quadruplex in complex with N-methyl mesoporphyrin IX
ComponentsDNA (5'-D(*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-tetrad
Function / homologyN-METHYLMESOPORPHYRIN / DNA / DNA (> 10)
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsChen, E.V. / Beseiso, D. / Yatsunyk, L.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R15CA253134 United States
CitationJournal: To Be Published
Title: Biophysical and structural characterization of telomeric G-quadruplexes from Tetrahymena thermophila in complex with N-Methyl Mesoporphyrin IX
Authors: Beseiso, D. / Chen, E.V. / Yatsunyk, L.A.
History
DepositionJun 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 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: DNA (5'-D(*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)8,5889
Polymers7,6561
Non-polymers9328
Water21612
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.284, 34.716, 34.397
Angle α, β, γ (deg.)90.000, 106.537, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-104-

NA

21A-105-

NA

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Components

#1: DNA chain DNA (5'-D(*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: 7655.879 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Tetrahymena thermophila (eukaryote)
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MMP / N-METHYLMESOPORPHYRIN


Mass: 580.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H40N4O4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Nonpolymer detailsThe authors state that the MPD ligands modelled in the structure are shown to have LINKS to the ...The authors state that the MPD ligands modelled in the structure are shown to have LINKS to the main DNA chain. Rather than removing the MPD to eliminate the LINKS, they have preserved the MPDs in the structure as a part of the crystal packing interaction. It should be noted that the MPD molecules are at symmetry-positions and have a high amount of disorder.

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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: 1.93 Å3/Da / Density % sol: 34.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Well condition contained 100 mM NaCl, 100 mM NaI, 100 mM NaF, 30% MPD, and 50 mM Na cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 196 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.98→32.97 Å / Num. obs: 3905 / % possible obs: 96.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 52.83 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.075 / Rrim(I) all: 0.14 / Net I/σ(I): 9.5
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 689 / CC1/2: 0.836 / Rpim(I) all: 0.599 / % possible all: 73.1

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
Coot0.8.9.2model building
XDSdata reduction
XDSdata scaling
PHENIX1.18_3845phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W9P

6w9p


Resolution: 1.99→32.97 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.4912
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2532 175 4.6 %
Rwork0.241 3627 -
obs0.2418 3802 94.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.61 Å2
Refinement stepCycle: LAST / Resolution: 1.99→32.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 467 54 12 533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051576
X-RAY DIFFRACTIONf_angle_d1.3333893
X-RAY DIFFRACTIONf_chiral_restr0.040490
X-RAY DIFFRACTIONf_plane_restr0.005625
X-RAY DIFFRACTIONf_dihedral_angle_d36.019220
LS refinement shellResolution: 1.99→32.97 Å
RfactorNum. reflection% reflection
Rfree0.2532 175 -
Rwork0.241 3627 -
obs--94.53 %
Refinement TLS params.Method: refined / Origin x: -4.19725759583 Å / Origin y: 7.41567938218 Å / Origin z: 9.3528971543 Å
111213212223313233
T0.596521197793 Å20.00448578445695 Å2-0.00219731053472 Å2-0.947281998961 Å20.0415379743272 Å2--0.411906991905 Å2
L2.92128441936 °2-0.839407510369 °2-3.8224923163 °2-7.25856694949 °21.8548696016 °2--8.77770046082 °2
S-0.0817096209032 Å °0.483867860062 Å °-0.0852755957012 Å °-0.826937479667 Å °0.132845146053 Å °0.00821057723449 Å °-0.161615121504 Å °-0.31699467677 Å °-0.103995897421 Å °
Refinement TLS groupSelection details: all

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