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- PDB-8ebo: Homopurine parallel G-quadruplex from human chromosome 7 stabiliz... -

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Basic information

Entry
Database: PDB / ID: 8ebo
TitleHomopurine parallel G-quadruplex from human chromosome 7 stabilized by K+ ions
ComponentsDNA (5'-D(*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*AP*AP*AP*GP*GP*GP*GP*A)-3')
KeywordsDNA / G-quadruplex / parallel / propeller loops
Function / homologyCOBALT (III) ION / : / N-METHYLMESOPORPHYRIN / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsChen, E.V. / Yatsunyk, L.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R15CA253134 United States
CitationJournal: Bioorg.Med.Chem. / Year: 2022
Title: Homopurine guanine-rich sequences in complex with N-methyl mesoporphyrin IX form parallel G-quadruplex dimers and display a unique symmetry tetrad.
Authors: Ye, M. / Chen, E.V. / Pfeil, S.H. / Martin, K.N. / Atrafi, T. / Yun, S. / Martinez, Z. / Yatsunyk, L.A.
History
DepositionAug 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: 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(*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*AP*AP*AP*GP*GP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8276
Polymers7,0701
Non-polymers7575
Water724
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)42.053, 47.474, 119.597
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Space group name HallF22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x,y+1/2,z+1/2
#6: x,-y+1/2,-z+1/2
#7: -x,y+1/2,-z+1/2
#8: -x,-y+1/2,z+1/2
#9: x+1/2,y,z+1/2
#10: x+1/2,-y,-z+1/2
#11: -x+1/2,y,-z+1/2
#12: -x+1/2,-y,z+1/2
#13: x+1/2,y+1/2,z
#14: x+1/2,-y+1/2,-z
#15: -x+1/2,y+1/2,-z
#16: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-105-

3CO

21A-202-

HOH

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Components

#1: DNA chain DNA (5'-D(*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*AP*AP*AP*GP*GP*GP*GP*A)-3')


Mass: 7069.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-MMP / N-METHYLMESOPORPHYRIN


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


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-3CO / COBALT (III) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.18 Å3/Da / Density % sol: 43.6 % / Description: thin, well-ordered rhombuses
Crystal growTemperature: 285.15 K / Method: vapor diffusion, hanging drop
Details: The well condition included 0.012 M NaCl, 0.08-0.1 M KCl, 0.04 M sodium cacodylate pH 5.5, 45% MPD, and 0.002 M hexammine cobalt(III) chloride

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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: Dec 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.98→30.44 Å / Num. obs: 4296 / % possible obs: 99.2 % / Redundancy: 5.8 % / Biso Wilson estimate: 64.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.023 / Rrim(I) all: 0.054 / Net I/σ(I): 15.1
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 279 / CC1/2: 0.351 / Rpim(I) all: 0.894 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
Aimlessdata scaling
Coot0.8.9.2model building
PHENIX1.19.2_4158phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G0F

4g0f


Resolution: 1.98→24.71 Å / SU ML: 0.2268 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 45.9448
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2789 425 9.99 %
Rwork0.2314 3829 -
obs0.2362 4254 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.26 Å2
Refinement stepCycle: LAST / Resolution: 1.98→24.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 435 37 4 476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142530
X-RAY DIFFRACTIONf_angle_d1.9337823
X-RAY DIFFRACTIONf_chiral_restr0.068682
X-RAY DIFFRACTIONf_plane_restr0.012823
X-RAY DIFFRACTIONf_dihedral_angle_d36.279203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.270.35661380.29661242X-RAY DIFFRACTION97.87
2.27-2.850.3471410.36191278X-RAY DIFFRACTION99.51
2.86-24.710.26121460.20421309X-RAY DIFFRACTION96.94
Refinement TLS params.Method: refined / Origin x: -15.0484741614 Å / Origin y: 2.8269384339 Å / Origin z: -14.539514764 Å
111213212223313233
T0.725036053306 Å2-0.254114679539 Å20.274254950121 Å2-0.545266786161 Å20.0258571795824 Å2--0.801844313619 Å2
L7.21771039797 °20.62766346869 °2-1.00812691194 °2-5.13867186864 °2-0.475429448416 °2--3.1501477118 °2
S-0.594130132333 Å °0.466286019956 Å °-0.875157920592 Å °-1.86782205107 Å °0.488663282853 Å °-2.13708530652 Å °0.645045189978 Å °0.702718040884 Å °0.380776529808 Å °
Refinement TLS groupSelection details: all

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