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- PDB-6e81: Crystal structure of the Corn aptamer in complex with ThT -

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Basic information

Entry
Database: PDB / ID: 6.0E+81
TitleCrystal structure of the Corn aptamer in complex with ThT
ComponentsRNA (36-MER)
KeywordsRNA / polyribonucleotide / fluorigenic aptamer / G-quadruplex / thioflavin T
Function / homology: / Chem-TFX / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.721 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)12,1173
Polymers11,7941
Non-polymers3232
Water00
1
A: RNA (36-MER)
hetero molecules

A: RNA (36-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2336
Polymers23,5882
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)131.404, 131.404, 40.632
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: RNA chain RNA (36-MER)


Mass: 11794.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: 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
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K

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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: 2.86 Å3/Da / Density % sol: 57.02 % / Description: rectangular plate-shaped
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 4000, 5% PEG400, 0.2M ammonium acetate pH 6.7, 0.1 M sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.72→66.26 Å / Num. obs: 3756 / % possible obs: 99.4 % / Redundancy: 38.5 % / Biso Wilson estimate: 85.56 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.011 / Rrim(I) all: 0.069 / Net I/σ(I): 25.1 / Num. measured all: 144541 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) all% possible allRmerge(I) obsRrim(I) all
2.72-2.7940.82750.3451.27798.8
12.17-66.2634.95110.00499.20.0230.023

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.35 Å38.32 Å
Translation3.35 Å38.32 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.5.27data scaling
PHASER2.7.16phasing
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BJP

5bjp


Resolution: 2.721→38.266 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 41.59
RfactorNum. reflection% reflection
Rfree0.259 369 10.17 %
Rwork0.2481 --
obs0.2494 3629 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 185.23 Å2 / Biso mean: 111.852 Å2 / Biso min: 55.75 Å2
Refinement stepCycle: final / Resolution: 2.721→38.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 785 41 0 826
Biso mean--67.75 --
Num. residues----36
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006924
X-RAY DIFFRACTIONf_angle_d1.2241438
X-RAY DIFFRACTIONf_chiral_restr0.055180
X-RAY DIFFRACTIONf_plane_restr0.00742
X-RAY DIFFRACTIONf_dihedral_angle_d21.1433
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 (%)
2.7208-3.11430.37981170.33751081119899
3.1143-3.92310.33931290.2751059118898
3.9231-38.26970.21961230.2261120124399
Refinement TLS params.Method: refined / Origin x: 1.9361 Å / Origin y: 50.9448 Å / Origin z: 20.1079 Å
111213212223313233
T0.4202 Å20.7988 Å2-0.0171 Å2-2.1706 Å2-0.1022 Å2--0.9266 Å2
L0.2479 °20.0454 °20.0931 °2-0.0047 °20.0561 °2--0.0839 °2
S-0.1008 Å °0.5513 Å °0.1966 Å °-0.0584 Å °0.4011 Å °0.1721 Å °-0.6301 Å °-2.1287 Å °-0.0534 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 36
2X-RAY DIFFRACTION1allC1
3X-RAY DIFFRACTION1allD1

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