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

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Basic information

Entry
Database: PDB / ID: 7xhd
TitleCrystal structure of a dimeric interlocked parallel G-quadruplex
ComponentsDNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*TP*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: 1.66 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 8, 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*TP*GP*GP*TP*GP*GP*GP*T)-3')
B: DNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*TP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4407
Polymers10,2452
Non-polymers1955
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.403, 30.917, 31.584
Angle α, β, γ (deg.)98.185, 97.150, 109.125
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*TP*GP*GP*TP*GP*GP*GP*T)-3')


Mass: 5122.284 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.: 99 / 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: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.002 M Copper(II) chloride dihydrate, 0.05 M TRIS hydrochloride pH 8.5, 1.8 M Lithium sulfate monohydrate, 0.0005 M Spermine

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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: 1.66→24.54 Å / Num. obs: 11663 / % possible obs: 96.23 % / Redundancy: 3.6 % / Biso Wilson estimate: 21.13 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.76
Reflection shellResolution: 1.66→1.72 Å / Num. unique obs: 1117 / CC1/2: 0.935

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Processing

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

7xdh


Resolution: 1.66→24.54 Å / SU ML: 0.1489 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 25.3003
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2116 1172 10.08 %
Rwork0.182 10455 -
obs0.185 11627 96.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.89 Å2
Refinement stepCycle: LAST / Resolution: 1.66→24.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 682 5 99 786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076768
X-RAY DIFFRACTIONf_angle_d0.97961192
X-RAY DIFFRACTIONf_chiral_restr0.0462126
X-RAY DIFFRACTIONf_plane_restr0.008632
X-RAY DIFFRACTIONf_dihedral_angle_d31.8931312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.740.2461420.22411256X-RAY DIFFRACTION91.97
1.74-1.830.24691470.23041299X-RAY DIFFRACTION95.57
1.83-1.940.24011440.20461293X-RAY DIFFRACTION96.31
1.94-2.090.24921470.19671317X-RAY DIFFRACTION96.7
2.09-2.30.24331460.20631304X-RAY DIFFRACTION97.38
2.3-2.630.21911460.20191347X-RAY DIFFRACTION97.45
2.64-3.320.25941540.21521308X-RAY DIFFRACTION96.95
3.32-24.540.1511460.13451331X-RAY DIFFRACTION97.88
Refinement TLS params.Method: refined / Origin x: -0.614512080543 Å / Origin y: -2.66999630187 Å / Origin z: 14.6700661252 Å
111213212223313233
T0.235572382628 Å2-0.00470339861743 Å20.00163292379396 Å2-0.233993677641 Å20.0141327562983 Å2--0.223933528982 Å2
L0.758724335676 °2-0.44829605353 °2-0.152306372666 °2-0.45931515329 °2-0.15428566813 °2--0.418665431008 °2
S-0.0391509769419 Å °0.0309479476835 Å °-0.027608475203 Å °0.0134730450774 Å °0.0121461446721 Å °-0.0370070627909 Å °0.039441484923 Å °-0.0127919038868 Å °-5.75474896611E-5 Å °
Refinement TLS groupSelection details: all

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