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- PDB-9ebp: Structure of the Bacillus subtilis yjdF riboswitch complexed with... -

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Basic information

Entry
Database: PDB / ID: 9ebp
TitleStructure of the Bacillus subtilis yjdF riboswitch complexed with lumichrome in the presence of iridium hexammine
ComponentsRNA (81-MER)
KeywordsRNA / riboswitch / aptamer / lumichrome / iridium hexammine / yjdF / azaaromatic
Function / homologyIRIDIUM HEXAMMINE ION / LUMICHROME / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 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 152029 United States
CitationJournal: To Be Published
Title: Structure of the Bacillus subtilis yjdF riboswitch complexed with lumichrome in the presence of iridium hexammine
Authors: Batey, R.T. / Spradlin, S.F.
History
DepositionNov 12, 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)55,85414
Polymers52,4252
Non-polymers3,42812
Water37821
1
A: RNA (81-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2218
Polymers26,2131
Non-polymers2,0097
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
M: RNA (81-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6326
Polymers26,2131
Non-polymers1,4205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.572, 65.817, 81.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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.) synthetic construct (others)
#2: 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
#3: Chemical
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: H18IrN6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5% MPD, 3 mM spermine, 50 mM Na-cacodylate pH 7.0, 20 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.1055 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1055 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 16987 / % possible obs: 99.7 % / Redundancy: 13.7 % / CC1/2: 1 / CC star: 1 / Rpim(I) all: 0.025 / Rsym value: 0.091 / Net I/σ(I): 43.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 12.4 % / Num. unique obs: 1635 / CC1/2: 0.815 / CC star: 0.948 / Rpim(I) all: 0.347 / Rsym value: 1.211 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data scaling
HKL-3000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→45.989 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2898 3126 9.93 %
Rwork0.2475 --
obs0.2519 16987 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→45.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3476 106 21 3603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013991
X-RAY DIFFRACTIONf_angle_d1.1596270
X-RAY DIFFRACTIONf_dihedral_angle_d13.8691922
X-RAY DIFFRACTIONf_chiral_restr0.029808
X-RAY DIFFRACTIONf_plane_restr0.003164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.74220.58661310.51841195X-RAY DIFFRACTION93
2.7422-2.78720.52181340.48481265X-RAY DIFFRACTION99
2.7872-2.83520.50651450.46921305X-RAY DIFFRACTION99
2.8352-2.88680.63011460.41531312X-RAY DIFFRACTION100
2.8868-2.94230.43831410.37951293X-RAY DIFFRACTION100
2.9423-3.00230.32391460.3291313X-RAY DIFFRACTION100
3.0023-3.06760.40071370.31151271X-RAY DIFFRACTION100
3.0676-3.13890.32721430.29441299X-RAY DIFFRACTION99
3.1389-3.21740.31611430.28441261X-RAY DIFFRACTION99
3.2174-3.30440.30951390.26651309X-RAY DIFFRACTION99
3.3044-3.40160.30811390.25131304X-RAY DIFFRACTION99
3.4016-3.51140.30091410.23951271X-RAY DIFFRACTION99
3.5114-3.63680.24341470.22691309X-RAY DIFFRACTION100
3.6368-3.78240.231390.20671283X-RAY DIFFRACTION100
3.7824-3.95440.26591450.19741297X-RAY DIFFRACTION100
3.9544-4.16280.23461430.19741316X-RAY DIFFRACTION100
4.1628-4.42340.25331420.20021290X-RAY DIFFRACTION100
4.4234-4.76460.20761440.20981319X-RAY DIFFRACTION100
4.7646-5.24350.21451470.21451276X-RAY DIFFRACTION100
5.2435-6.00080.25351450.22331289X-RAY DIFFRACTION100
6.0008-7.55490.27121460.24171305X-RAY DIFFRACTION100
7.5549-45.9890.34411430.25011268X-RAY DIFFRACTION97

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