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- PDB-9bun: RhoBAST aptamer RNA in complex with 5(6)-carboxytetramethylrhodamine -

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Basic information

Entry
Database: PDB / ID: 9bun
TitleRhoBAST aptamer RNA in complex with 5(6)-carboxytetramethylrhodamine
ComponentsRNA (48-MER)
KeywordsRNA / aptamer / fluorophore / dye / TAMRA
Function / homology5-carboxy methylrhodamine / IRIDIUM HEXAMMINE ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsBatey, R.T. / Siwik, S.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM133184 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
DepositionMay 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (48-MER)
B: RNA (48-MER)
C: RNA (48-MER)
D: RNA (48-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,48723
Polymers62,3464
Non-polymers6,14219
Water8,341463
1
A: RNA (48-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9015
Polymers15,5861
Non-polymers1,3154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (48-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1956
Polymers15,5861
Non-polymers1,6095
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA (48-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4907
Polymers15,5861
Non-polymers1,9036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA (48-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9015
Polymers15,5861
Non-polymers1,3154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.424, 174.242, 87.791
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-285-

HOH

21D-302-

HOH

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Components

#1: RNA chain
RNA (48-MER)


Mass: 15586.393 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: H18IrN6
#3: Chemical
ChemComp-FH8 / 5-carboxy methylrhodamine


Mass: 431.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H23N2O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 3.22 Å3/Da / Density % sol: 61.8 % / Description: elongated prism
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 40 mM sodium cacodylate, 12 mM sodium chloride, 80 mM potassium chloride, 5% MPD, 20 mM spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0972 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0972 Å / Relative weight: 1
ReflectionResolution: 1.95→44.45 Å / Num. obs: 58528 / % possible obs: 99.9 % / Redundancy: 64.1 % / CC1/2: 1 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.013 / Rrim(I) all: 0.103 / Χ2: 1.03 / Net I/σ(I): 34.2 / Num. measured all: 3750599
Reflection shellResolution: 1.95→2 Å / % possible obs: 99.7 % / Redundancy: 46.3 % / Rmerge(I) obs: 8.15 / Num. measured all: 188221 / Num. unique obs: 4067 / CC1/2: 0.319 / Rpim(I) all: 1.18 / Rrim(I) all: 8.239 / Χ2: 0.94 / Net I/σ(I) obs: 0.6

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Processing

Software
NameVersionClassification
PHENIX1.14-3260-000refinement
Aimlessdata scaling
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→44.236 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.26 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2406 3040 3.43 %
Rwork0.2164 --
obs0.2172 46132 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→44.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4144 233 463 4840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034874
X-RAY DIFFRACTIONf_angle_d0.6277673
X-RAY DIFFRACTIONf_dihedral_angle_d13.4412304
X-RAY DIFFRACTIONf_chiral_restr0.031960
X-RAY DIFFRACTIONf_plane_restr0.005212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13280.37071450.32023802X-RAY DIFFRACTION100
2.1328-2.16780.3361440.31323907X-RAY DIFFRACTION100
2.1678-2.20520.32231350.30443913X-RAY DIFFRACTION100
2.2052-2.24530.40451360.31743885X-RAY DIFFRACTION100
2.2453-2.28850.41591280.30973862X-RAY DIFFRACTION100
2.2885-2.33520.31681390.27943889X-RAY DIFFRACTION100
2.3352-2.38590.28981430.27623893X-RAY DIFFRACTION100
2.3859-2.44140.32871420.27763901X-RAY DIFFRACTION100
2.4414-2.50250.35341320.26563892X-RAY DIFFRACTION100
2.5025-2.57010.29971350.25753911X-RAY DIFFRACTION100
2.5701-2.64580.32211390.26563843X-RAY DIFFRACTION100
2.6458-2.73110.30771410.27343915X-RAY DIFFRACTION100
2.7311-2.82870.3081340.28743889X-RAY DIFFRACTION100
2.8287-2.9420.2361470.26573876X-RAY DIFFRACTION100
2.942-3.07580.36911310.23523884X-RAY DIFFRACTION100
3.0758-3.2380.23951370.21533893X-RAY DIFFRACTION100
3.238-3.44080.23631390.20823890X-RAY DIFFRACTION100
3.4408-3.70630.21441390.19143880X-RAY DIFFRACTION100
3.7063-4.0790.21191440.19013905X-RAY DIFFRACTION100
4.079-4.66870.20071300.18533888X-RAY DIFFRACTION100
4.6687-5.87990.17741380.17783895X-RAY DIFFRACTION100
5.8799-44.2360.20951420.19683883X-RAY DIFFRACTION100

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