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

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Basic information

Entry
Database: PDB / ID: 7kvv
TitleCrystal structure of Squash RNA aptamer in complex with DFHBI-1T
ComponentsSquash RNA aptamer bound to DFHO
KeywordsRNA / fluorogenic aptamer / adenine riboswitch
Function / homologyChem-747 / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 1.2Oct 18, 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
D: Squash RNA aptamer bound to DFHO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3174
Polymers26,9871
Non-polymers3303
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.271, 104.271, 52.107
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
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 DFHO


Mass: 26986.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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.: 1 / Source method: obtained synthetically / Formula: C12H9F2N3O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
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, and 40 mM NaI

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→52.14 Å / Num. obs: 7090 / % possible obs: 99.9 % / Redundancy: 31.4 % / Biso Wilson estimate: 109.76 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 93.1
Reflection shellResolution: 2.85→2.95 Å / Rmerge(I) obs: 3.458 / Num. unique obs: 611

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KVT

7kvt


Resolution: 2.85→52.14 Å / SU ML: 0.5774 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.5695
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.245 710 10.01 %
Rwork0.221 6380 -
obs0.2226 7090 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.8 Å2
Refinement stepCycle: LAST / Resolution: 2.85→52.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1788 21 2 1811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00112020
X-RAY DIFFRACTIONf_angle_d0.39823146
X-RAY DIFFRACTIONf_chiral_restr0.0184414
X-RAY DIFFRACTIONf_plane_restr0.001585
X-RAY DIFFRACTIONf_dihedral_angle_d14.2584998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.070.54281390.44761248X-RAY DIFFRACTION98.51
3.07-3.380.29361350.26321223X-RAY DIFFRACTION99.93
3.38-3.870.27881400.25471257X-RAY DIFFRACTION99.86
3.87-4.870.27741430.23881287X-RAY DIFFRACTION100
4.88-52.140.20421530.18481365X-RAY DIFFRACTION99.93

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