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- PDB-9l8f: Crystal structure of RhoBAST aptamer in complex with TMR -

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Basic information

Entry
Database: PDB / ID: 9l8f
TitleCrystal structure of RhoBAST aptamer in complex with TMR
ComponentsRNA (57-MER)
KeywordsRNA / Aptamer / RhoBAST / TMR
Function / homology: / SELENIUM ATOM / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å
AuthorsTai, X.Q. / Ren, A.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of RhoBAST aptamer in complex with TMR
Authors: Tai, X.Q. / Ren, A.M.
History
DepositionDec 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
U: RNA (57-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,58712
Polymers18,5741
Non-polymers1,01311
Water18010
1
U: RNA (57-MER)
hetero molecules

U: RNA (57-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,17424
Polymers37,1482
Non-polymers2,02622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area3430 Å2
ΔGint-104 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.462, 84.462, 107.316
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11U-105-

SE

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Components

#1: RNA chain RNA (57-MER)


Mass: 18574.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
#2: Chemical
ChemComp-SE / SELENIUM ATOM


Mass: 78.960 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Se
#3: Chemical ChemComp-A1EI4 / [9-(2-carboxyphenyl)-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium / 9-(2-carboxyphenyl)-3,6-bis(dimethylamino)xanthylium


Mass: 387.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.13 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.01 M Magnesium sulfate heptahydrate, 0.05 M Sodium cacodylate trihydrate pH 7.1, 2.2 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.51→43.27 Å / Num. obs: 36717 / % possible obs: 94.5 % / Redundancy: 35.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 41.1
Reflection shellResolution: 2.51→2.65 Å / Num. unique obs: 36717 / CC1/2: 0.818

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.51→30.22 Å / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.26 660 4.77 %
Rwork0.2294 --
obs0.2312 13843 94.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→30.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1233 39 10 1282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d1.262
X-RAY DIFFRACTIONf_dihedral_angle_d16.537706
X-RAY DIFFRACTIONf_chiral_restr0.059284
X-RAY DIFFRACTIONf_plane_restr0.00975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.650.61271200.53932061X-RAY DIFFRACTION99
2.71-2.980.38131380.382734X-RAY DIFFRACTION100
2.98-3.410.29231250.28532810X-RAY DIFFRACTION100
3.41-4.290.28221410.22592777X-RAY DIFFRACTION100
4.29-30.220.18951360.16192801X-RAY DIFFRACTION100

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