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- PDB-8f0n: Wobble Beetroot (A16U-U38G) dimer bound to DFHO -

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Basic information

Entry
Database: PDB / ID: 8f0n
TitleWobble Beetroot (A16U-U38G) dimer bound to DFHO
ComponentsRNA (49-MER)
KeywordsRNA / aptamer / fluorescence / turn-on / fluorogenic / fluorophore / G-quartet / G-quadruplex
Function / homologyChem-747 / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsPassalacqua, L.F.M. / Ferre-D'Amare, A.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: Nat Commun / Year: 2023
Title: Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture.
Authors: Passalacqua, L.F.M. / Starich, M.R. / Link, K.A. / Wu, J. / Knutson, J.R. / Tjandra, N. / Jaffrey, S.R. / Ferre-D'Amare, A.R.
History
DepositionNov 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: RNA (49-MER)
A: RNA (49-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8379
Polymers32,0792
Non-polymers7587
Water63135
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.012, 50.353, 94.584
Angle α, β, γ (deg.)90.000, 95.703, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: RNA chain RNA (49-MER)


Mass: 16039.509 Da / Num. of mol.: 2 / Mutation: A16U, U38G / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-747 / (5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-2-[(E)-(hydroxyimino)methyl]-3-methyl-3,5-dihydro-4H-imidazol-4-one


Mass: 281.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9F2N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4 M Ammonium sulfate, 5% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→94.12 Å / Num. obs: 6710 / % possible obs: 99.88 % / Redundancy: 6.4 % / Biso Wilson estimate: 42.69 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.295 / Rpim(I) all: 0.126 / Rrim(I) all: 0.321 / Net I/σ(I): 2.5
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.186 / Num. unique obs: 617 / CC1/2: 0.482 / % possible all: 90.47

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Coot0.9.5model building
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8EYU

8eyu


Resolution: 2.85→47.06 Å / SU ML: 0.4284 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.1153
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.256 677 10.23 %
Rwork0.194 5942 -
obs0.2004 6619 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.48 Å2
Refinement stepCycle: LAST / Resolution: 2.85→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2073 45 35 2153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652361
X-RAY DIFFRACTIONf_angle_d1.15153682
X-RAY DIFFRACTIONf_chiral_restr0.051481
X-RAY DIFFRACTIONf_plane_restr0.005699
X-RAY DIFFRACTIONf_dihedral_angle_d20.01011164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.070.34381160.29721144X-RAY DIFFRACTION95.09
3.07-3.380.26991470.21731182X-RAY DIFFRACTION98.81
3.38-3.870.26281570.19061160X-RAY DIFFRACTION99.55
3.87-4.870.22881320.15961209X-RAY DIFFRACTION100
4.87-47.060.23331250.17391247X-RAY DIFFRACTION99.85
Refinement TLS params.Method: refined / Origin x: 5.72681320393 Å / Origin y: -7.68783291633 Å / Origin z: 3.92979116507 Å
111213212223313233
T0.16818885429 Å20.00936192931996 Å2-0.131928689248 Å2--0.0357701229434 Å20.0312370528781 Å2--0.321363222079 Å2
L3.69680105544 °20.148128899638 °20.0324656948284 °2-2.16202417411 °2-0.747983250527 °2--1.11437050926 °2
S0.000887485970283 Å °-0.120768956054 Å °-0.154119121601 Å °0.237412381506 Å °-0.0535739981794 Å °-0.0139189521474 Å °0.0633318186876 Å °0.0349378988542 Å °-0.122145307086 Å °
Refinement TLS groupSelection details: all

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