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- PDB-5kx9: Selective Small Molecule Inhibition of the FMN Riboswitch -

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Basic information

Entry
Database: PDB / ID: 5kx9
TitleSelective Small Molecule Inhibition of the FMN Riboswitch
Components(FMN Riboswitch) x 2
KeywordsRNA/inhibitor / RNA / TRANSLATION / RNA-inhibitor complex
Function / homologyChem-6YG / : / : / RNA / RNA (> 10)
Function and homology information
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.9 Å
AuthorsFischmann, T.O.
Citation
Journal: Rna Biol. / Year: 2016
Title: Atomic resolution mechanistic studies of ribocil: A highly selective unnatural ligand mimic of the E. coli FMN riboswitch.
Authors: Howe, J.A. / Xiao, L. / Fischmann, T.O. / Wang, H. / Tang, H. / Villafania, A. / Zhang, R. / Barbieri, C.M. / Roemer, T.
#1: Journal: Nature / Year: 2015
Title: Selective small-molecule inhibition of an RNA structural element.
Authors: Howe, J.A. / Wang, H. / Fischmann, T.O. / Balibar, C.J. / Xiao, L. / Galgoci, A.M. / Malinverni, J.C. / Mayhood, T. / Villafania, A. / Nahvi, A. / Murgolo, N. / Barbieri, C.M. / Mann, P.A. / ...Authors: Howe, J.A. / Wang, H. / Fischmann, T.O. / Balibar, C.J. / Xiao, L. / Galgoci, A.M. / Malinverni, J.C. / Mayhood, T. / Villafania, A. / Nahvi, A. / Murgolo, N. / Barbieri, C.M. / Mann, P.A. / Carr, D. / Xia, E. / Zuck, P. / Riley, D. / Painter, R.E. / Walker, S.S. / Sherborne, B. / de Jesus, R. / Pan, W. / Plotkin, M.A. / Wu, J. / Rindgen, D. / Cummings, J. / Garlisi, C.G. / Zhang, R. / Sheth, P.R. / Gill, C.J. / Tang, H. / Roemer, T.
History
DepositionJul 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Oct 19, 2016Group: Database references
Revision 1.3Feb 22, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: FMN Riboswitch
Y: FMN Riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,30314
Polymers35,5482
Non-polymers75412
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-56 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.280, 71.280, 138.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: RNA chain FMN Riboswitch /


Mass: 17455.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Fusobacterium nucleatum (bacteria) / References: GenBank: 777193512
#2: RNA chain FMN Riboswitch /


Mass: 18092.771 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Fusobacterium nucleatum (bacteria) / References: GenBank: 777193512
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-6YG / (6P)-2-{(3S)-1-[(2-methoxypyrimidin-5-yl)methyl]piperidin-3-yl}-6-(thiophen-2-yl)pyrimidin-4-ol


Mass: 383.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N5O2S

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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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1 M NA ACETATE, PH 5.0, 0.2 M MGCL2, 7 TO 11% V/V PEG 4K
PH range: 4.5-6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→46.03 Å / Num. obs: 9428 / % possible obs: 98.8 % / Redundancy: 9.3 % / Biso Wilson estimate: 101.72 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Net I/σ(I): 22.3
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.799 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
DENZOdata reduction
SCALEPACK0.1.27data scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5C45

5c45


Resolution: 2.9→37.04 Å / Cor.coef. Fo:Fc: 0.9366 / Cor.coef. Fo:Fc free: 0.9069 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.378
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 458 4.86 %RANDOM
Rwork0.216 ---
obs0.2177 9425 98.89 %-
Displacement parametersBiso mean: 98.93 Å2
Baniso -1Baniso -2Baniso -3
1-3.5062 Å20 Å20 Å2
2--3.5062 Å20 Å2
3----7.0124 Å2
Refine analyzeLuzzati coordinate error obs: 0.477 Å
Refinement stepCycle: 1 / Resolution: 2.9→37.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2321 38 0 2359
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012628HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.764090HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d546SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes110HARMONIC5
X-RAY DIFFRACTIONt_it2628HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion24.2
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion432SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2622SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.24 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3088 134 5.04 %
Rwork0.2607 2526 -
all0.2629 2660 -
obs--98.89 %

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