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- PDB-7dfy: Novel motif for left-handed G-quadruplex formation -

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Basic information

Entry
Database: PDB / ID: 7dfy
TitleNovel motif for left-handed G-quadruplex formation
Components2xMotif2
KeywordsDNA / Left-handed / G-quadruplex / Bulge / four-layer
Function / homology: / STRONTIUM ION / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsDas, P. / Winnerdy, F.R. / Maity, A. / Mechulam, Y. / Phan, A.T.
Funding support Singapore, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-NRFI2017-09 Singapore
Ministry of Education (MoE, Singapore)MOE2015-T2-1-092 Singapore
CitationJournal: Chem.Commun.(Camb.) / Year: 2021
Title: A novel minimal motif for left-handed G-quadruplex formation.
Authors: Das, P. / Winnerdy, F.R. / Maity, A. / Mechulam, Y. / Phan, A.T.
History
DepositionNov 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: 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: 2xMotif2
B: 2xMotif2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,86523
Polymers16,5292
Non-polymers1,33721
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, Formed four-layer G-quadruplex structure
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-237 kcal/mol
Surface area7340 Å2
Unit cell
Length a, b, c (Å)28.405, 31.601, 77.764
Angle α, β, γ (deg.)90.000, 98.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain 2xMotif2 / DNA (26-mer)


Mass: 8264.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA motif for left-handed G-quadruplex formation / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Sr
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.09 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.08 M Strontium Chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate ph=6.0, 35% v/v (+/-)-2-Methyl-2,4-pentanediol (MPD), 0.012 M Spermine tetrahydrochoride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.69→76.995 Å / Num. obs: 9010 / % possible obs: 86.2 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.08 / Rrim(I) all: 0.206 / Net I/σ(I): 8
Reflection shellResolution: 1.69→1.904 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.212 / Mean I/σ(I) obs: 1 / Num. unique obs: 450 / CC1/2: 0.349 / Rpim(I) all: 0.739 / % possible all: 40.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6gz6

6gz6


Resolution: 1.69→76.99 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 437 4.86 %
Rwork0.201 8557 -
obs0.2039 8994 57.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.53 Å2 / Biso mean: 21.7197 Å2 / Biso min: 0.7 Å2
Refinement stepCycle: final / Resolution: 1.69→76.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1098 29 80 1207
Biso mean--27 16.39 -
Num. residues----52
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.69-1.930.3988210.296858260312
1.94-2.440.30771420.24152985312761
2.44-76.990.24052740.18249905264100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7367-0.07940.05360.73070.08780.4873-0.0009-0.13940.16470.0208-0.0306-0.016-0.0369-0.02160.01860.05710.00290.01610.038-0.01710.06862.9459-7.6168.6295
20.78870.19860.67921.25340.22491.45260.1498-0.6329-0.19420.66920.0215-0.13770.23030.1827-0.10080.3075-0.0098-0.04610.40940.04450.143315.8751-16.618325.9104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 1:26)A1 - 26
2X-RAY DIFFRACTION2(chain B and resseq 1:26)B1 - 26

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