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- PDB-8d78: Crystal structure of a Ba stabilized four-tetrad, parallel Tetrah... -

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Entry
Database: PDB / ID: 8d78
TitleCrystal structure of a Ba stabilized four-tetrad, parallel Tetrahymena thermophila telomeric G-quadruplex in complex with N-methyl mesoporphyrin IX
ComponentsDNA (5'-D(*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*G)-3')
KeywordsDNA / G-quadruplex / Parallel / Four-quartets
Function / homology: / N-METHYLMESOPORPHYRIN / DNA / DNA (> 10)
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9034
Polymers7,0471
Non-polymers8553
Water37821
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)35.081, 35.081, 103.191
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Space group name HallP322(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: -y,-x,-z+1/3
#5: -x+y,y,-z+2/3
#6: x,x-y,-z
Components on special symmetry positions
IDModelComponents
11A-207-

HOH

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Components

#1: DNA chain DNA (5'-D(*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*G)-3')


Mass: 7047.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Tetrahymena thermophila (eukaryote)
#2: Chemical ChemComp-MMP / N-METHYLMESOPORPHYRIN


Mass: 580.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H40N4O4
#3: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Well condition contained 0.6-1 M sodium formate, 12-16% PEG 20K, 0.05 M Bis Tris pH 7.0

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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: 2.12→103.19 Å / Num. obs: 4315 / % possible obs: 98.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 50.54 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.061 / Rrim(I) all: 0.127 / Net I/σ(I): 6.9
Reflection shellResolution: 2.12→2.18 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.071 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 368 / CC1/2: 0.727 / Rpim(I) all: 0.552 / % possible all: 100

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Processing

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

6w9p


Resolution: 2.12→34.4 Å / SU ML: 0.3294 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 46.8543
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2644 413 9.83 %
Rwork0.2552 3788 -
obs0.2561 4201 96.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.17 Å2
Refinement stepCycle: LAST / Resolution: 2.12→34.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 469 35 21 525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037565
X-RAY DIFFRACTIONf_angle_d1.2326878
X-RAY DIFFRACTIONf_chiral_restr0.024587
X-RAY DIFFRACTIONf_plane_restr0.004226
X-RAY DIFFRACTIONf_dihedral_angle_d31.8194216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.430.40881400.39671272X-RAY DIFFRACTION99.02
2.43-3.050.39531350.33461247X-RAY DIFFRACTION96.98
3.06-34.40.21051380.21551269X-RAY DIFFRACTION94.24
Refinement TLS params.Method: refined / Origin x: -3.15747664525 Å / Origin y: -1.41894852123 Å / Origin z: -7.9814105706 Å
111213212223313233
T0.846342890728 Å2-0.534618242171 Å20.0148338642986 Å2-1.01363180031 Å2-0.0467287237319 Å2--0.657330994113 Å2
L4.17660403149 °2-2.93420540017 °2-1.17370440418 °2-6.41528118339 °20.278478139921 °2--5.99429387288 °2
S-0.315065490677 Å °-0.0311163660774 Å °0.184706609891 Å °-0.670635890838 Å °0.571252881273 Å °-0.21643307368 Å °-0.498904168496 Å °0.128658017117 Å °-0.142469284061 Å °
Refinement TLS groupSelection details: all

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