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

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Basic information

Entry
Database: PDB / ID: 7xdh
TitleCrystal structure of a dimeric interlocked parallel G-quadruplex
ComponentsDNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*AP*GP*GP*AP*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: 1.83 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 27, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,95214
Polymers20,5614
Non-polymers39110
Water88349
1
A: DNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*AP*GP*GP*AP*GP*GP*GP*T)-3')
B: DNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*AP*GP*GP*AP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4767
Polymers10,2812
Non-polymers1955
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*AP*GP*GP*AP*GP*GP*GP*T)-3')
D: DNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*AP*GP*GP*AP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4767
Polymers10,2812
Non-polymers1955
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.685, 30.340, 56.493
Angle α, β, γ (deg.)79.024, 83.357, 78.197
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*AP*GP*GP*AP*GP*GP*GP*T)-3')


Mass: 5140.312 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.05 Å3/Da / Density % sol: 40.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.08 M Sodium chloride, 0.02 M Magnesium chloride hexahydrate, 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 9M / 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: 1.826→29.26 Å / Num. obs: 13916 / % possible obs: 95.01 % / Redundancy: 4.2 % / Biso Wilson estimate: 35.69 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.98
Reflection shellResolution: 1.826→1.857 Å / Num. unique obs: 1413 / CC1/2: 0.962

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata scaling
PHENIX1.19.2-4158-000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y8D

1y8d


Resolution: 1.83→29.26 Å / SU ML: 0.2319 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 37.2734
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2532 1384 10.04 %
Rwork0.2269 12397 -
obs0.2297 13781 94.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.94 Å2
Refinement stepCycle: LAST / Resolution: 1.83→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1352 10 49 1411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811530
X-RAY DIFFRACTIONf_angle_d0.94012374
X-RAY DIFFRACTIONf_chiral_restr0.0444248
X-RAY DIFFRACTIONf_plane_restr0.005663
X-RAY DIFFRACTIONf_dihedral_angle_d33.8938614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.890.39251400.31171263X-RAY DIFFRACTION95.7
1.89-1.970.33021180.30091055X-RAY DIFFRACTION80.95
1.97-2.060.40061360.28871228X-RAY DIFFRACTION96.06
2.06-2.160.30521440.27621279X-RAY DIFFRACTION95.63
2.16-2.30.29661370.28141226X-RAY DIFFRACTION95.12
2.3-2.480.30821410.25781263X-RAY DIFFRACTION97.3
2.48-2.730.28131410.24111264X-RAY DIFFRACTION96.9
2.73-3.120.2741430.26461286X-RAY DIFFRACTION97.48
3.12-3.930.24211420.22091248X-RAY DIFFRACTION96.59
3.93-29.260.20491420.18081285X-RAY DIFFRACTION98.01
Refinement TLS params.Method: refined / Origin x: 4.84774730784 Å / Origin y: -2.51563985782 Å / Origin z: -24.786644211 Å
111213212223313233
T0.183970213026 Å20.036021042857 Å2-0.0420549147186 Å2-0.212012335815 Å2-0.0311141584518 Å2--0.305827552321 Å2
L2.30709406657 °20.701609846225 °2-0.921613588769 °2-1.68200029577 °2-1.31867781028 °2--5.09564212723 °2
S0.00165477511459 Å °0.114016783634 Å °-0.0278929003702 Å °0.0452953484 Å °-0.0046898446066 Å °0.0260841161698 Å °-0.120378679021 Å °-0.0343970144546 Å °-0.0160475172786 Å °
Refinement TLS groupSelection details: all

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