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- PDB-6e82: Crystal structure of the Corn aptamer mutant A14U in complex with ThT -

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Basic information

Entry
Database: PDB / ID: 6.0E+82
TitleCrystal structure of the Corn aptamer mutant A14U in complex with ThT
ComponentsRNA (36-MER)
KeywordsRNA / polyribonucleotide / fluorigenic aptamer / G-quadruplex / thioflavin T / Corn mutant A14U
Function / homology: / Chem-TFX / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.101 Å
AuthorsSjekloca, L. / Ferre-D'Amare, A.R.
CitationJournal: Cell Chem Biol / Year: 2019
Title: Binding between G Quadruplexes at the Homodimer Interface of the Corn RNA Aptamer Strongly Activates Thioflavin T Fluorescence.
Authors: Sjekloca, L. / Ferre-D'Amare, A.R.
History
DepositionJul 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (36-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0943
Polymers11,7711
Non-polymers3232
Water00
1
A: RNA (36-MER)
hetero molecules

A: RNA (36-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1876
Polymers23,5422
Non-polymers6454
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_556-x+2/3,-x+y+1/3,-z+4/31
Unit cell
Length a, b, c (Å)130.723, 130.723, 40.674
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-102-

TFX

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Components

#1: RNA chain RNA (36-MER)


Mass: 11771.060 Da / Num. of mol.: 1 / Mutation: A14U / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-TFX / 2-[4-(dimethylamino)phenyl]-3,6-dimethyl-1,3-benzothiazol-3-ium / Thioflavin T


Mass: 283.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N2S

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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: 2.84 Å3/Da / Density % sol: 56.7 % / Description: rectangular plate-shaped
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 20 % PEG 4000, 5% PEG 400, 10% glycerol, 0.2 M ammonium acetate pH 6.7, 0.1 M sodium citrate pH 5.6, 0.5 mM ThT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.96→37.74 Å / Num. obs: 2840 / % possible obs: 99.9 % / Redundancy: 19 % / Biso Wilson estimate: 75.66 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.032 / Rrim(I) all: 0.141 / Net I/σ(I): 13.8 / Num. measured all: 53903 / Scaling rejects: 45
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.96-3.0419.11.0621980.5160.2461.091100
13.24-37.7415.50.0183610.0050.01896

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å38.28 Å
Translation3 Å38.28 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.27data scaling
PHASER2.7.16phasing
PDB_EXTRACT3.24data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BJP

5bjp


Resolution: 3.101→33.031 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.59 / Phase error: 24.76
RfactorNum. reflection% reflection
Rfree0.3298 246 10 %
Rwork0.238 --
obs0.2475 2459 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 184.27 Å2 / Biso mean: 108.9614 Å2 / Biso min: 63.98 Å2
Refinement stepCycle: final / Resolution: 3.101→33.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 783 41 0 824
Biso mean--74.16 --
Num. residues----36
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008921
X-RAY DIFFRACTIONf_angle_d1.6881433
X-RAY DIFFRACTIONf_chiral_restr0.066180
X-RAY DIFFRACTIONf_plane_restr0.00842
X-RAY DIFFRACTIONf_dihedral_angle_d22.025433
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1011-3.9060.36821200.29851083120399
3.906-33.03270.31411260.212811301256100
Refinement TLS params.Method: refined / Origin x: 1.8666 Å / Origin y: 50.7071 Å / Origin z: 20.137 Å
111213212223313233
T0.0712 Å20.6819 Å2-0.0834 Å2-2.6112 Å2-0.1542 Å2--0.864 Å2
L0.3649 °20.3158 °2-0.4063 °2-0.3755 °2-0.1074 °2--0.8673 °2
S0.2857 Å °1.0915 Å °0.2262 Å °0.0552 Å °-0.2081 Å °0.0306 Å °-0.8172 Å °-1.6858 Å °0.0049 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 36
2X-RAY DIFFRACTION1allD2
3X-RAY DIFFRACTION1allB1

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