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- PDB-7xie: Crystal structure of a dimeric interlocked parallel G-quadruplex -

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Basic information

Entry
Database: PDB / ID: 7xie
TitleCrystal structure of a dimeric interlocked parallel G-quadruplex
ComponentsDNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*GP*GP*GP*TP*GP*GP*GP*T)-3')
KeywordsDNA / G-quadruplex / interlocked
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsNgo, K.H. / Liew, C.W. / Lattmann, S. / Winnerdy, F.R. / Phan, A.T.
Funding support Singapore, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-NRFI2017-09 Singapore
Ministry of Education (MoE, Singapore)MOE2018-T2-2-029 Singapore
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Crystal structures of an HIV-1 integrase aptamer: Formation of a water-mediated A•G•G•G•G pentad in an interlocked G-quadruplex.
Authors: Ngo, K.H. / Liew, C.W. / Lattmann, S. / Winnerdy, F.R. / Phan, A.T.
History
DepositionApr 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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*GP*GP*GP*GP*GP*GP*TP*GP*GP*GP*T)-3')
B: DNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*GP*GP*GP*TP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5689
Polymers10,2952
Non-polymers2747
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-0 kcal/mol
Surface area5740 Å2
Unit cell
Length a, b, c (Å)26.577, 29.628, 29.584
Angle α, β, γ (deg.)63.689, 78.160, 78.185
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: DNA chain DNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*GP*GP*GP*TP*GP*GP*GP*T)-3')


Mass: 5147.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 1.97 Å3/Da / Density % sol: 37.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.08 M Potassium chloride, 0.02 M Barium chloride dihydrate, 0.04 M Sodium cacodylate trihydrate pH 7.0, 40% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953659 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953659 Å / Relative weight: 1
ReflectionResolution: 1.97→26.33 Å / Num. obs: 5377 / % possible obs: 96.63 % / Redundancy: 3.5 % / Biso Wilson estimate: 32.29 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.63
Reflection shellResolution: 1.97→2.04 Å / Num. unique obs: 521 / CC1/2: 0.95

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XDH

7xdh


Resolution: 1.97→26.33 Å / SU ML: 0.3026 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 33.0618
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.237 543 10.17 %
Rwork0.2073 4795 -
obs0.2104 5338 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.55 Å2
Refinement stepCycle: LAST / Resolution: 1.97→26.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 686 7 37 730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074774
X-RAY DIFFRACTIONf_angle_d0.93111202
X-RAY DIFFRACTIONf_chiral_restr0.0529126
X-RAY DIFFRACTIONf_plane_restr0.005232
X-RAY DIFFRACTIONf_dihedral_angle_d34.1244312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.170.32911270.24951166X-RAY DIFFRACTION95.64
2.17-2.480.27921400.24981213X-RAY DIFFRACTION96.64
2.48-3.130.25291400.23971213X-RAY DIFFRACTION97.13
3.13-26.330.20491360.17561203X-RAY DIFFRACTION97.17

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