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- PDB-6e84: Crystal structure of the Corn aptamer in complex with TO -

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Basic information

Entry
Database: PDB / ID: 6.0E+84
TitleCrystal structure of the Corn aptamer in complex with TO
ComponentsRNA (36-MER)
KeywordsRNA / polyribonucleotide / fluorigenic aptamer / G-quadruplex / thiazole orange
Function / homologyChem-J0D / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.901 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)12,1393
Polymers11,7941
Non-polymers3452
Water00
1
A: RNA (36-MER)
hetero molecules

A: RNA (36-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2776
Polymers23,5882
Non-polymers6894
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)128.611, 128.611, 40.843
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-

J0D

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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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-J0D / 1-methyl-4-[(Z)-(3-methyl-1,3-benzothiazol-2(3H)-ylidene)methyl]quinolin-1-ium / Thiazole orange


Mass: 305.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17N2S

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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: 2.75 Å3/Da / Density % sol: 55.35 %
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 thiazole orange

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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: Apr 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→38.35 Å / Num. obs: 3104 / % possible obs: 100 % / Redundancy: 18.9 % / Biso Wilson estimate: 80.05 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.02 / Rrim(I) all: 0.088 / Net I/σ(I): 16.3 / Num. measured all: 58519 / Scaling rejects: 65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.85-2.92181.0492440.6840.251.079100
12.75-38.3515.50.0284210.0070.02898

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.72 Å64.29 Å
Translation4.72 Å64.29 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: 6.0E+81 / Resolution: 2.901→38.346 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 25.67
RfactorNum. reflection% reflection
Rfree0.2931 293 9.98 %
Rwork0.2345 --
obs0.2401 2937 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 382.08 Å2 / Biso mean: 130.8393 Å2 / Biso min: 45.83 Å2
Refinement stepCycle: final / Resolution: 2.901→38.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 785 23 0 808
Biso mean--72.19 --
Num. residues----36
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008905
X-RAY DIFFRACTIONf_angle_d1.4511410
X-RAY DIFFRACTIONf_chiral_restr0.063180
X-RAY DIFFRACTIONf_plane_restr0.00938
X-RAY DIFFRACTIONf_dihedral_angle_d20.792431
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9011-3.65470.36391440.294813031447
3.6547-38.34950.27121490.214813411490
Refinement TLS params.Method: refined / Origin x: 1.8221 Å / Origin y: 23.97 Å / Origin z: 7.1348 Å
111213212223313233
T0.2342 Å2-0.6335 Å20.0008 Å2-1.7129 Å2-0.3018 Å2--0.6205 Å2
L0.2038 °2-0.0707 °20.0898 °2-0.0275 °2-0.0138 °2--0.3009 °2
S0.2034 Å °-0.4164 Å °-0.1207 Å °0.0366 Å °-0.0958 Å °-0.0795 Å °0.5816 Å °-1.5486 Å °0.1333 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 36
2X-RAY DIFFRACTION1allD1
3X-RAY DIFFRACTION1allC1

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