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- PDB-8eyu: Structure of Beetroot dimer bound to DFAME -

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Basic information

Entry
Database: PDB / ID: 8eyu
TitleStructure of Beetroot dimer bound to DFAME
ComponentsRNA (49-MER)
KeywordsRNA / aptamer / fluorescence / turn-on / fluorogenic / fluorophore / G-quartet / G-quadruplex
Function / homology: / Chem-X5R / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
B: RNA (49-MER)
A: RNA (49-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8879
Polymers32,0472
Non-polymers8407
Water2,666148
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)29.937, 50.742, 95.555
Angle α, β, γ (deg.)90.000, 94.083, 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: 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: obtained synthetically / Formula: K
#3: Chemical ChemComp-X5R / methyl (2E)-3-{(4Z)-4-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-1-methyl-5-oxo-4,5-dihydro-1H-imidazol-2-yl}prop-2-enoate


Mass: 322.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12F2N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.26 Å3/Da / Density % sol: 45.55 % / Description: Plate-shaped crystals
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2 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: 0.977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.95→47.66 Å / Num. obs: 21035 / % possible obs: 99.82 % / Redundancy: 6.5 % / Biso Wilson estimate: 23.26 Å2 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.061 / Net I/σ(I): 16.32
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 2095 / CC1/2: 0.985

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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: 5BJO

5bjo


Resolution: 1.95→47.66 Å / SU ML: 0.1815 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 20.0807
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.204 1998 9.51 %
Rwork0.1784 19001 -
obs0.1809 20999 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.61 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2027 51 148 2226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00352317
X-RAY DIFFRACTIONf_angle_d0.81763611
X-RAY DIFFRACTIONf_chiral_restr0.0449465
X-RAY DIFFRACTIONf_plane_restr0.0063104
X-RAY DIFFRACTIONf_dihedral_angle_d18.18021147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.26141300.21581377X-RAY DIFFRACTION99.87
2-2.050.22021390.20521311X-RAY DIFFRACTION99.72
2.05-2.110.21691290.17731396X-RAY DIFFRACTION100
2.11-2.180.21751230.18581359X-RAY DIFFRACTION99.8
2.18-2.260.21111600.18721311X-RAY DIFFRACTION100
2.26-2.350.19011620.18891343X-RAY DIFFRACTION100
2.35-2.460.19931320.17871366X-RAY DIFFRACTION100
2.46-2.590.21741340.18851345X-RAY DIFFRACTION100
2.59-2.750.24121590.20191337X-RAY DIFFRACTION99.6
2.75-2.960.261430.20911369X-RAY DIFFRACTION100
2.96-3.260.18751490.17761349X-RAY DIFFRACTION99.67
3.26-3.730.18831440.17121360X-RAY DIFFRACTION99.14
3.73-4.70.17481340.15461376X-RAY DIFFRACTION100
4.7-47.660.19551600.16271402X-RAY DIFFRACTION99.87
Refinement TLS params.Method: refined / Origin x: 4.96521452588 Å / Origin y: -7.21539058635 Å / Origin z: 2.70785937178 Å
111213212223313233
T0.107338249967 Å20.00567935845445 Å20.0599247103386 Å2-0.121619038615 Å2-0.0131663713993 Å2--0.234744844803 Å2
L3.76983118148 °2-0.0707617444351 °20.293602735461 °2-2.73751322175 °2-0.0959645928474 °2--1.75405280809 °2
S-0.0602752141357 Å °-0.105198396549 Å °-0.0981709114457 Å °-0.00808298423866 Å °0.0647371246484 Å °-0.112406333923 Å °0.0643342015902 Å °-0.0237319941536 Å °-0.0276883615541 Å °
Refinement TLS groupSelection details: all

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