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- PDB-8g2n: Crystal structure of Tetrahymena thermophila G-rich DNA with nove... -

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Basic information

Entry
Database: PDB / ID: 8g2n
TitleCrystal structure of Tetrahymena thermophila G-rich DNA with novel ligand PyDH2
ComponentsG-rich DNA
KeywordsDNA / G-quadruplex DNA / ligand intercalation / four tetrads
Function / homology: / SPERMINE / : / DNA / DNA (> 10)
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsMartin, K.N. / 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: Crystal structure of Tetrahymena thermophila G-rich DNA with novel ligand PyDH2
Authors: Martin, K.N. / Yatsunyk, L.A.
History
DepositionFeb 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: G-rich DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8337
Polymers7,9851
Non-polymers8476
Water1,13563
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)38.332, 47.314, 87.106
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-260-

HOH

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Components

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DNA chain , 1 types, 1 molecules A

#1: DNA chain G-rich DNA


Mass: 7985.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Tetrahymena thermophila (eukaryote)

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Non-polymers , 5 types, 69 molecules

#2: Chemical ChemComp-YSQ / 4,4'-{pyridine-2,6-diylbis[carbonyl-(1E)-hydrazin-2-yl-1-ylidene-(E)-methanylylidene]}bis(1-methylquinolin-1-ium)


Mass: 503.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H25N7O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.6 % / Description: Flat golden rhombus
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.02 M MgCl2, 0.165 M KCl, 0.04 M sodium cacodylate pH 6.5, 0.012 M spermine tetrahydrochloride, 39% (+/-)-2-Methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.33→29.78 Å / Num. obs: 18082 / % possible obs: 97.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 24.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.026 / Net I/σ(I): 24.7
Reflection shellResolution: 1.33→1.35 Å / Redundancy: 5.1 % / Num. unique obs: 818 / CC1/2: 0.758 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158phasing
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→29.78 Å / SU ML: 0.1461 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.1518
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1939 862 4.78 %
Rwork0.1719 17155 -
obs0.173 18017 96.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.46 Å2
Refinement stepCycle: LAST / Resolution: 1.33→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 531 56 63 650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0186703
X-RAY DIFFRACTIONf_angle_d1.83531079
X-RAY DIFFRACTIONf_chiral_restr0.093107
X-RAY DIFFRACTIONf_plane_restr0.021434
X-RAY DIFFRACTIONf_dihedral_angle_d31.5753284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.410.26041280.26542664X-RAY DIFFRACTION91.54
1.41-1.520.28751410.24362766X-RAY DIFFRACTION94.75
1.52-1.680.2191480.1642878X-RAY DIFFRACTION99.05
1.68-1.920.18891400.15592918X-RAY DIFFRACTION98.93
1.92-2.420.221390.2112930X-RAY DIFFRACTION98.9
2.42-29.780.17951660.15822999X-RAY DIFFRACTION97.69

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