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- PDB-8edp: Crystal structure of a three-tetrad, parallel, and K+ stabilized ... -

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Basic information

Entry
Database: PDB / ID: 8edp
TitleCrystal structure of a three-tetrad, parallel, and K+ stabilized homopurine G-quadruplex from human chromosome 7
ComponentsDNA (5'-D(*AP*GP*GP*GP*AP*AP*AP*AP*GP*GP*GP*GP*AP*GP*GP*GP*AP*AP*AP*AP*GP*GP*GP*G)-3')
KeywordsDNA / G-quadruplex / parallel / propeller loops / three-tetrad
Function / homology: / N-METHYLMESOPORPHYRIN / COBALT HEXAMMINE(III) / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsYe, M. / 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
DepositionSep 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,9077
Polymers8,0091
Non-polymers8986
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-0 kcal/mol
Surface area5150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.583, 40.927, 56.018
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-105-

K

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Components

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


Mass: 8009.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-MMP / N-METHYLMESOPORPHYRIN


Mass: 580.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H40N4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
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: 2.25 Å3/Da / Density % sol: 45.5 %
Description: Red crystals in cubic, rhombus, or square prism shapes
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: 0.05M MES 6.5, 0.3M potassium chloride, 40% MPD, 0.005M Hexaammine cobalt 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 EIGER2 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: 2.01→56.02 Å / Num. obs: 5027 / % possible obs: 98.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 62.16 Å2 / CC1/2: 0.986 / Net I/σ(I): 8.8
Reflection shellResolution: 2.01→2.06 Å / Num. unique obs: 374 / CC1/2: 0.447

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
Aimless1.19.2_4158data scaling
Coot0.9.6model building
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G0F

4g0f


Resolution: 2.01→28.01 Å / SU ML: 0.3468 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 45.99
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2781 497 9.99 %
Rwork0.2432 4476 -
obs0.2468 4973 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.87 Å2
Refinement stepCycle: LAST / Resolution: 2.01→28.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 472 44 5 521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083576
X-RAY DIFFRACTIONf_angle_d1.4832898
X-RAY DIFFRACTIONf_chiral_restr0.038392
X-RAY DIFFRACTIONf_plane_restr0.008824
X-RAY DIFFRACTIONf_dihedral_angle_d34.1241230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.210.43751210.3731094X-RAY DIFFRACTION99.02
2.21-2.530.34891220.30531098X-RAY DIFFRACTION99.35
2.53-3.190.33091240.30561115X-RAY DIFFRACTION98.88
3.19-28.010.24991300.21481169X-RAY DIFFRACTION98.11
Refinement TLS params.Method: refined / Origin x: 2.76191104192 Å / Origin y: 15.4476523302 Å / Origin z: 4.58538821286 Å
111213212223313233
T0.400865420473 Å20.0355730058433 Å20.0086329612202 Å2-0.535133595573 Å20.128500554488 Å2--0.446232659791 Å2
L7.28805699095 °21.732883136 °2-0.337139431567 °2-9.60754369905 °22.7890431099 °2--9.27446782266 °2
S0.0196716831373 Å °-0.143297067281 Å °0.072263839968 Å °0.324655474228 Å °-0.258104213831 Å °0.366386467567 Å °0.11663700269 Å °0.594211897316 Å °0.0630329815375 Å °
Refinement TLS groupSelection details: all

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