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- PDB-5c45: Selective Small Molecule Inhibition of the FMN Riboswitch -

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Basic information

Entry
Database: PDB / ID: 5c45
TitleSelective Small Molecule Inhibition of the FMN Riboswitch
Components(FMN Riboswitch) x 2
KeywordsRNA/INHIBITOR / RNA / TRANSLATION / RNA-INHIBITOR complex
Function / homologyChem-51B / : / : / RNA / RNA (> 10)
Function and homology information
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsFischmann, T.O.
CitationJournal: 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
DepositionJun 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Mar 1, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _chem_comp.name / _citation.journal_id_CSD ..._chem_comp.name / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_ref_seq_dif.details
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)36,21411
Polymers35,5482
Non-polymers6669
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-39 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.110, 71.110, 138.510
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: 20095250
#2: RNA chain FMN Riboswitch


Mass: 18092.771 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Fusobacterium nucleatum (bacteria) / References: GenBank: 20095250
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-51B / (6M)-2-[(3S)-1-{[2-(methylamino)pyrimidin-5-yl]methyl}piperidin-3-yl]-6-(thiophen-2-yl)pyrimidin-4-ol


Mass: 382.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N6OS

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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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M Na Acetate, pH 5.0, 0.2 M MgCl2, and 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: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.928→35.6 Å / Num. obs: 9222 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 109.83 Å2 / Rmerge(I) obs: 0.019 / Net I/σ(I): 36.2
Reflection shellResolution: 2.928→2.938 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.16 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F4E

3f4e


Resolution: 2.93→35.56 Å / Cor.coef. Fo:Fc: 0.9377 / Cor.coef. Fo:Fc free: 0.9218 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.362
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 442 4.82 %RANDOM
Rwork0.2128 ---
obs0.2138 9179 99.97 %-
Displacement parametersBiso mean: 103.14 Å2
Baniso -1Baniso -2Baniso -3
1-6.946 Å20 Å20 Å2
2--6.946 Å20 Å2
3----13.892 Å2
Refine analyzeLuzzati coordinate error obs: 0.485 Å
Refinement stepCycle: 1 / Resolution: 2.93→35.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2340 35 0 2375
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012649HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.744123HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d551SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes112HARMONIC5
X-RAY DIFFRACTIONt_it2649HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion23.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion436SEMIHARMONIC5
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_contact2634SEMIHARMONIC4
LS refinement shellResolution: 2.93→3.28 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2705 126 4.98 %
Rwork0.2513 2402 -
all0.2522 2528 -
obs--99.97 %

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