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- PDB-9dxl: RhoBAST RNA aptamer in complex with the SpyRho555 analogue, MaP555 -

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Basic information

Entry
Database: PDB / ID: 9dxl
TitleRhoBAST RNA aptamer in complex with the SpyRho555 analogue, MaP555
ComponentsRhoBAST aptamer
KeywordsRNA / aptamer / fluorophore / dye / MaP555
Function / homology: / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSiwik, S.H. / Batey, R.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2404117 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM152029 United States
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structural basis for ring-opening fluorescence by the RhoBAST RNA aptamer.
Authors: Siwik, S.H. / Wierzba, A.J. / Lennon, S.R. / Olenginski, L.T. / Palmer, A.E. / Batey, R.T.
History
DepositionOct 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RhoBAST aptamer
B: RhoBAST aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,94612
Polymers31,1732
Non-polymers1,77410
Water61334
1
A: RhoBAST aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9488
Polymers15,5861
Non-polymers1,3627
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RhoBAST aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9984
Polymers15,5861
Non-polymers4123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.529, 54.818, 83.513
Angle α, β, γ (deg.)90.000, 103.263, 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 RhoBAST aptamer


Mass: 15586.393 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: T7 RNA polymerase transcript of an in vitro selected aptamer
Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ba
#3: Chemical ChemComp-A1BC9 / 3-[3-(dimethylamino)-6-(dimethyl-$l^{4}-azanylidene)xanthen-9-yl]-4-(dimethylsulfamoylcarbamoyl)benzoic acid


Mass: 537.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29N4O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.88 Å3/Da / Density % sol: 57.4 % / Description: elongated prisms
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 40 mM MES, 10 mM barium chloride, 80 mM potassium chloride, 25% MPD, 12 mM spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 7, 2024
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 8812 / % possible obs: 98 % / Redundancy: 2.7 % / Rpim(I) all: 0.074 / Rrim(I) all: 0.127 / Χ2: 1.541 / Net I/av σ(I): 11.56 / Net I/σ(I): 9.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.69 / Num. unique obs: 839 / CC1/2: 0.815 / CC star: 0.948 / Rpim(I) all: 0.074 / Rrim(I) all: 0.127 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.27 Å / Cross valid method: FREE R-VALUE / σ(F): 21.83 / Phase error: 40.8904
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2706 848 10.21 %Random
Rwork0.2539 7455 --
obs0.2629 8303 98.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.1 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2072 47 34 2153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00152363
X-RAY DIFFRACTIONf_angle_d0.49543682
X-RAY DIFFRACTIONf_chiral_restr0.0336480
X-RAY DIFFRACTIONf_plane_restr0.0042101
X-RAY DIFFRACTIONf_dihedral_angle_d19.80341150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.970.36921320.34851225X-RAY DIFFRACTION87.5
2.97-3.20.31921430.33721251X-RAY DIFFRACTION87.97
3.2-3.520.31221390.29391216X-RAY DIFFRACTION88.37
3.52-4.030.2891390.27491236X-RAY DIFFRACTION88.98
4.03-5.060.23191390.23831282X-RAY DIFFRACTION89.53
5.06-19.270.24211430.19911258X-RAY DIFFRACTION86.7

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