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- PDB-9ebv: Structure of the Bacillus subtilis yjdF riboswitch aptamer domain... -

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Basic information

Entry
Database: PDB / ID: 9ebv
TitleStructure of the Bacillus subtilis yjdF riboswitch aptamer domain in complex with lumichrome
ComponentsRNA (81-MER)
KeywordsRNA / riboswitch / flavin / aptamer
Function / homology: / LUMICHROME / RNA / RNA (> 10)
Function and homology information
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.519 Å
AuthorsBatey, R.T. / Spradlin, S.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM152029 United States
CitationJournal: To Be Published
Title: Structure of the Bacillus subtilis yjdF riboswitch aptamer domain in complex with lumichrome
Authors: Batey, R.T. / Spradlin, S.F.
History
DepositionNov 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (81-MER)
M: RNA (81-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,42621
Polymers52,4252
Non-polymers1,00119
Water1,27971
1
A: RNA (81-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,70810
Polymers26,2131
Non-polymers4969
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
M: RNA (81-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,71811
Polymers26,2131
Non-polymers50510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.718, 68.927, 82.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: RNA chain RNA (81-MER)


Mass: 26212.580 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-LUM / LUMICHROME / 7,8-DIMETHYLALLOXAZINE / 6,7-DIMETHYLALLOXAZINE


Mass: 242.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10N4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 6% MPD, 9 mM spermine, 40 mM Na-cacodylate pH 7.0, 20 mM KCl

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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: Apr 22, 2022
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 21630 / % possible obs: 97.4 % / Redundancy: 4.8 % / Rpim(I) all: 0.04 / Rsym value: 0.082 / Net I/σ(I): 20.63
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.4 % / Num. unique obs: 1685 / CC1/2: 0.854 / CC star: 0.96 / Rpim(I) all: 0.322 / Rsym value: 0.545 / % possible all: 77.6

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.519→19.793 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2463 1983 9.25 %
Rwork0.2157 --
obs0.2185 21434 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.519→19.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3476 53 71 3600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033931
X-RAY DIFFRACTIONf_angle_d0.7746120
X-RAY DIFFRACTIONf_dihedral_angle_d12.21922
X-RAY DIFFRACTIONf_chiral_restr0.035808
X-RAY DIFFRACTIONf_plane_restr0.005164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.519-2.58160.34831150.31961128X-RAY DIFFRACTION82
2.5816-2.65120.36831420.32571392X-RAY DIFFRACTION99
2.6512-2.72910.48341430.37141394X-RAY DIFFRACTION100
2.7291-2.81690.42041420.35981398X-RAY DIFFRACTION100
2.8169-2.91730.41841410.34521395X-RAY DIFFRACTION99
2.9173-3.03370.36731400.30181400X-RAY DIFFRACTION99
3.0337-3.17120.34461400.27651382X-RAY DIFFRACTION98
3.1712-3.33770.25761440.22521373X-RAY DIFFRACTION98
3.3377-3.54570.25441410.21881401X-RAY DIFFRACTION99
3.5457-3.81760.21931450.20611423X-RAY DIFFRACTION99
3.8176-4.19850.20251400.17911393X-RAY DIFFRACTION98
4.1985-4.79850.20711470.16961422X-RAY DIFFRACTION98
4.7985-6.01730.19061480.16121440X-RAY DIFFRACTION98
6.0173-19.7930.1781550.1741510X-RAY DIFFRACTION98

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