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- PDB-8eyv: Structure of Beetroot dimer bound to DFHO -

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Basic information

Entry
Database: PDB / ID: 8eyv
TitleStructure of Beetroot dimer bound to DFHO
ComponentsRNA (45-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: 2.55 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
DepositionOct 28, 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
A: RNA (45-MER)
B: RNA (45-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8059
Polymers32,0472
Non-polymers7587
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.790, 50.788, 97.088
Angle α, β, γ (deg.)90.000, 94.903, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: RNA chain RNA (45-MER)


Mass: 16023.509 Da / Num. of mol.: 2 / 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: isolated from a natural source / 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: isolated from a natural source / Formula: C12H9F2N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.0 M Ammonium sulfate, 5% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.104 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.104 Å / Relative weight: 1
ReflectionResolution: 2.55→96.73 Å / Num. obs: 9500 / % possible obs: 99.1 % / Redundancy: 6.5 % / Biso Wilson estimate: 42.97 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.139 / Net I/σ(I): 6.5
Reflection shellResolution: 2.55→2.64 Å / Num. unique obs: 915 / CC1/2: 0.966

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Processing

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

8eyu


Resolution: 2.55→48.37 Å / SU ML: 0.3087 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.2155
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: For the most disordered regions, the modeled nucleotides were refined with occupancy = 0. The list of nucleotides is: chain A - G1, C2, G48, C49, chain B - G6, C44, C47, and C49.
RfactorNum. reflection% reflection
Rfree0.21 908 9.59 %
Rwork0.183 8556 -
obs0.1965 9499 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.95 Å2
Refinement stepCycle: LAST / Resolution: 2.55→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1952 45 49 2046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642226
X-RAY DIFFRACTIONf_angle_d1.1963468
X-RAY DIFFRACTIONf_chiral_restr0.0597448
X-RAY DIFFRACTIONf_plane_restr0.007496
X-RAY DIFFRACTIONf_dihedral_angle_d20.4281072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.710.28131240.22971442X-RAY DIFFRACTION98.06
2.71-2.920.32161370.281407X-RAY DIFFRACTION99.29
2.92-3.210.26231630.20731419X-RAY DIFFRACTION99.18
3.21-3.680.23771510.20261431X-RAY DIFFRACTION98.32
3.68-4.630.16791660.16211397X-RAY DIFFRACTION98.8
4.63-48.370.1931670.17641460X-RAY DIFFRACTION98.73
Refinement TLS params.Method: refined / Origin x: 5.02849723171 Å / Origin y: -6.77033324989 Å / Origin z: 3.71842876319 Å
111213212223313233
T0.171454659106 Å20.01914279035 Å2-0.0236877741146 Å2-0.0953612776025 Å2-0.0476647394325 Å2--0.554355114973 Å2
L3.4256728706 °20.10235291996 °20.305756618098 °2-2.71498053952 °2-0.976017850471 °2--1.35220920525 °2
S0.07406911406 Å °-0.0536912306919 Å °-0.135250564601 Å °0.0430864329761 Å °0.0105285273919 Å °-0.121509858304 Å °0.0189669361176 Å °0.00383248181266 Å °-0.0802579135404 Å °
Refinement TLS groupSelection details: all

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