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- PDB-6bfb: Crystal structure of a F. nucleatum FMN riboswitch bound to WG-3 -

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Basic information

Entry
Database: PDB / ID: 6bfb
TitleCrystal structure of a F. nucleatum FMN riboswitch bound to WG-3
Components
  • RNA (54-MER)
  • RNA (56-MER)
KeywordsRNA / TRANSLATION / RNA-INHIBITOR COMPLEX
Function / homologyChem-DKM / RNA / RNA (> 10)
Function and homology information
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.82 Å
AuthorsRizvi, N.F. / Fischmann, T.O.
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Discovery of Selective RNA-Binding Small Molecules by Affinity-Selection Mass Spectrometry.
Authors: Rizvi, N.F. / Howe, J.A. / Nahvi, A. / Klein, D.J. / Fischmann, T.O. / Kim, H.Y. / McCoy, M.A. / Walker, S.S. / Hruza, A. / Richards, M.P. / Chamberlin, C. / Saradjian, P. / Butko, M.T. / ...Authors: Rizvi, N.F. / Howe, J.A. / Nahvi, A. / Klein, D.J. / Fischmann, T.O. / Kim, H.Y. / McCoy, M.A. / Walker, S.S. / Hruza, A. / Richards, M.P. / Chamberlin, C. / Saradjian, P. / Butko, M.T. / Mercado, G. / Burchard, J. / Strickland, C. / Dandliker, P.J. / Smith, G.F. / Nickbarg, E.B.
History
DepositionOct 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: RNA (54-MER)
Y: RNA (56-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0054
Polymers35,5482
Non-polymers4572
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-21 kcal/mol
Surface area16150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.130, 71.130, 141.190
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 RNA (54-MER)


Mass: 17455.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Fusobacterium nucleatum (bacteria)
#2: RNA chain RNA (56-MER)


Mass: 18092.771 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Fusobacterium nucleatum (bacteria)
#3: Chemical ChemComp-DKM / 5-[(3S,4S)-3-(dimethylamino)-4-hydroxypyrrolidin-1-yl]-6-fluoro-4-methyl-8-oxo-3,4-dihydro-8H-1-thia-4,9b-diazacyclopenta[cd]phenalene-9-carboxylic acid


Mass: 432.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21FN4O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 57.59 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate pH 5.5-6.5, 0.2 M MgCl2, 7-11% v/v PEG 4000
PH range: 5.5-6.5

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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: Mar 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.82→56.46 Å / Num. obs: 9904 / % possible obs: 94.3 % / Redundancy: 9.6 % / Biso Wilson estimate: 107.33 Å2 / Net I/σ(I): 32

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Processing

Software
NameVersionClassification
autoBUSTER2.11.7refinement
XDSdata reduction
autoPROCdata scaling
autoBUSTERphasing
RefinementResolution: 2.82→46.41 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 1.852 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.357 / SU Rfree Cruickshank DPI: 0.336
RfactorNum. reflection% reflectionSelection details
Rfree0.243 481 4.89 %RANDOM
Rwork0.203 ---
obs0.205 9842 94 %-
Displacement parametersBiso mean: 104.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.5343 Å20 Å20 Å2
2--0.5343 Å20 Å2
3----1.0687 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: 1 / Resolution: 2.82→46.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2340 31 12 2383
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012674HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.784181HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d549SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes140HARMONIC5
X-RAY DIFFRACTIONt_it2674HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion22.6
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_contact2629SEMIHARMONIC4
LS refinement shellResolution: 2.82→3.15 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3172 147 5.07 %
Rwork0.2259 2755 -
all0.23 2902 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.4604-0.9686-0.25392.4945-0.2982.30670.2351-0.0941-0.83630.24360.11660.3704-0.2646-0.1301-0.3517-0.3330.046-0.0264-0.2070.033-0.256226.566340.351915.7745
24.5424-0.94790.83912.4574-0.78952.43140.1724-0.1819-0.6270.5007-0.00760.3916-0.3327-0.2465-0.1649-0.3940.0350.0389-0.2372-0.0259-0.329922.95643.910617.0999
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ X|* }
2X-RAY DIFFRACTION2{ Y|* }

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