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- PDB-7kvt: Crystal structure of Squash RNA aptamer in complex with DFHBI-1T ... -

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Entry
Database: PDB / ID: 7kvt
TitleCrystal structure of Squash RNA aptamer in complex with DFHBI-1T with iridium (III) ions
ComponentsSquash RNA aptamer bound to DFHBI-1T with iridium (III) ions
KeywordsRNA / fluorogenic aptamer / adenine riboswitch
Function / homologyChem-2ZY / IRIDIUM HEXAMMINE ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.73 Å
AuthorsTruong, L. / 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.Chem.Biol. / Year: 2022
Title: The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold.
Authors: Truong, L. / Kooshapur, H. / Dey, S.K. / Li, X. / Tjandra, N. / Jaffrey, S.R. / Ferre-D'Amare, A.R.
History
DepositionNov 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Squash RNA aptamer bound to DFHBI-1T with iridium (III) ions
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2397
Polymers26,9871
Non-polymers1,2526
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.900, 103.900, 51.699
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: RNA chain Squash RNA aptamer bound to DFHBI-1T with iridium (III) ions


Mass: 26986.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-2ZY / (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one


Mass: 320.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9F5N2O2
#3: Chemical ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H18IrN6
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.59 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 40 mM Na cacodylate pH 7.0, 80 mM NaCl, 12 mM spermine hydrochloride, 36% (v/v) MPD, 40 mM NaI, and 1 mM iridium (III) hexammine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.105 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.105 Å / Relative weight: 1
ReflectionResolution: 2.73→46.5 Å / Num. obs: 7929 / % possible obs: 99.9 % / Redundancy: 24.7 % / Biso Wilson estimate: 81.37 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 69.6
Reflection shellResolution: 2.73→2.9 Å / Rmerge(I) obs: 3.114 / Num. unique obs: 1386

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.73→46.47 Å / SU ML: 0.408 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.374
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.251 791 9.98 %
Rwork0.209 --
obs0.213 7929 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.1 Å2
Refinement stepCycle: LAST / Resolution: 2.73→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1788 45 6 1839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072047
X-RAY DIFFRACTIONf_angle_d1.5133212
X-RAY DIFFRACTIONf_dihedral_angle_d16.586999
X-RAY DIFFRACTIONf_chiral_restr0.062414
X-RAY DIFFRACTIONf_plane_restr0.00885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.90.43991280.33381155X-RAY DIFFRACTION100
2.9-3.120.37371280.28981153X-RAY DIFFRACTION100
3.13-3.440.28411290.23031175X-RAY DIFFRACTION100
3.44-3.940.25151300.22751169X-RAY DIFFRACTION100
3.94-4.960.26971340.21181202X-RAY DIFFRACTION100
4.96-46.470.19611420.17171284X-RAY DIFFRACTION100

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