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- PDB-7x7g: Crystal structure of a dimeric interlocked parallel G-quadruplex -

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Basic information

Entry
Database: PDB / ID: 7x7g
TitleCrystal structure of a dimeric interlocked parallel G-quadruplex
ComponentsDNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*AP*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: 2.19 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
DepositionMar 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*AP*GP*GP*TP*GP*GP*GP*T)-3')
B: DNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*AP*GP*GP*TP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4587
Polymers10,2632
Non-polymers1955
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint7 kcal/mol
Surface area5160 Å2
Unit cell
Length a, b, c (Å)26.173, 31.247, 49.893
Angle α, β, γ (deg.)90.000, 102.899, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 5131.297 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.: 5 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 1.94 Å3/Da / Density % sol: 36.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.01 M magnesium chloride hexahydrate, 0.05 M HEPES sodium pH 7.5, 15% v/v (+/-)-2-methyl-2,4-pentanediol, 0.0015 M spermine

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.19→48.63 Å / Num. obs: 8264 / % possible obs: 97.56 % / Redundancy: 2 % / Biso Wilson estimate: 27.47 Å2 / CC1/2: 1 / Net I/σ(I): 9.82
Reflection shellResolution: 2.19→2.268 Å / Num. unique obs: 4149 / CC1/2: 0.985

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158-000refinement
autoPROCdata processing
autoPROCdata scaling
PHENIX1.19.2-4158-000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y8D

1y8d


Resolution: 2.19→48.63 Å / SU ML: 0.1756 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 37.5678
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2685 765 9.87 %
Rwork0.256 6983 -
obs0.2575 7748 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.87 Å2
Refinement stepCycle: LAST / Resolution: 2.19→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 684 5 39 728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009770
X-RAY DIFFRACTIONf_angle_d2.0231190
X-RAY DIFFRACTIONf_chiral_restr0.1891126
X-RAY DIFFRACTIONf_plane_restr0.005132
X-RAY DIFFRACTIONf_dihedral_angle_d33.0353306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.360.33711590.33121428X-RAY DIFFRACTION98.08
2.36-2.590.29841570.27971401X-RAY DIFFRACTION98.3
2.59-2.970.31961550.30981364X-RAY DIFFRACTION96.26
2.97-3.740.24931480.25851408X-RAY DIFFRACTION96.77
3.74-48.630.22121460.20541382X-RAY DIFFRACTION96.95

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