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- PDB-8d2b: Crystal structure of theophylline aptamer in complex with TAL2 -

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Basic information

Entry
Database: PDB / ID: 8d2b
TitleCrystal structure of theophylline aptamer in complex with TAL2
ComponentsRNA (33-MER)
KeywordsRNA / aptamer / theophylline
Function / homologyChem-QAX / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsMenichelli, E. / Spraggon, G.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Discovery of small molecules that target a tertiary-structured RNA.
Authors: Menichelli, E. / Lam, B.J. / Wang, Y. / Wang, V.S. / Shaffer, J. / Tjhung, K.F. / Bursulaya, B. / Nguyen, T.N. / Vo, T. / Alper, P.B. / McAllister, C.S. / Jones, D.H. / Spraggon, G. / ...Authors: Menichelli, E. / Lam, B.J. / Wang, Y. / Wang, V.S. / Shaffer, J. / Tjhung, K.F. / Bursulaya, B. / Nguyen, T.N. / Vo, T. / Alper, P.B. / McAllister, C.S. / Jones, D.H. / Spraggon, G. / Michellys, P.Y. / Joslin, J. / Joyce, G.F. / Rogers, J.
History
DepositionMay 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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: RNA (33-MER)
B: RNA (33-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,12313
Polymers21,2752
Non-polymers84811
Water5,747319
1
A: RNA (33-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0496
Polymers10,6371
Non-polymers4125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA (33-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0747
Polymers10,6371
Non-polymers4366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)23.074, 29.567, 80.309
Angle α, β, γ (deg.)95.660, 91.510, 109.960
Int Tables number1
Space group name H-MP1

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Components

#1: RNA chain RNA (33-MER)


Mass: 10637.426 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-QAX / 6-methoxy-7-[3-(piperidin-1-yl)propoxy]quinazolin-4-ol


Mass: 317.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: sodium cacodylate, PEG 8000, 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.44→20.34 Å / Num. obs: 33441 / % possible obs: 93.35 % / Redundancy: 3.8 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.0705 / Rpim(I) all: 0.0424 / Net I/σ(I): 11.26
Reflection shellResolution: 1.441→1.492 Å / Num. unique obs: 2581 / CC1/2: 0.835

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1O15

1o15


Resolution: 1.44→20.34 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 1721 5.15 %
Rwork0.2009 31699 -
obs0.2022 33420 93.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.28 Å2 / Biso mean: 20.5825 Å2 / Biso min: 3.6 Å2
Refinement stepCycle: final / Resolution: 1.44→20.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1408 101 319 1828
Biso mean--25.47 24.96 -
Num. residues----66
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.44-1.480.30511110.25281918202969
1.48-1.530.25981500.24512694284494
1.53-1.590.25211540.24592601275594
1.59-1.650.27421520.23282715286794
1.65-1.720.24941360.21792665280195
1.72-1.810.25581380.20872714285296
1.81-1.930.21141430.20312721286495
1.93-2.080.22971330.20382725285896
2.08-2.290.20261580.19242724288296
2.29-2.620.23581420.21142736287897
2.62-3.290.22971470.20662763291097
3.29-20.340.19411570.16122723288097

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