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- PDB-6dn2: CRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1354 SPLIT RNA -

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Basic information

Entry
Database: PDB / ID: 6dn2
TitleCRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1354 SPLIT RNA
Components
  • RNA (56-MER)
  • RNA RIBOSWITCH
KeywordsRNA / FMN / RIBOSWITCH / TRANSCRIPTION
Function / homologyChem-GZG / : / RNA / RNA (> 10)
Function and homology information
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsVicens, Q. / Mondragon, E. / Reyes, F.E. / Berman, J. / Kaur, H. / Kells, K. / Wickens, P. / Wilson, J. / Gadwood, R. / Schostarez, H. ...Vicens, Q. / Mondragon, E. / Reyes, F.E. / Berman, J. / Kaur, H. / Kells, K. / Wickens, P. / Wilson, J. / Gadwood, R. / Schostarez, H. / Suto, R.K. / Coish, P. / Blount, K.F. / Batey, R.T.
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Structure-Activity Relationship of Flavin Analogues That Target the Flavin Mononucleotide Riboswitch.
Authors: Vicens, Q. / Mondragon, E. / Reyes, F.E. / Coish, P. / Aristoff, P. / Berman, J. / Kaur, H. / Kells, K.W. / Wickens, P. / Wilson, J. / Gadwood, R.C. / Schostarez, H.J. / Suto, R.K. / Blount, K.F. / Batey, R.T.
History
DepositionJun 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 31, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,19510
Polymers35,5482
Non-polymers6468
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-53 kcal/mol
Surface area15960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.070, 71.070, 140.480
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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RNA chain , 2 types, 2 molecules XY

#1: RNA chain RNA RIBOSWITCH


Mass: 17455.389 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: IN VITRO TRANSCRIBED RNA FROM FUSOBACTERIUM NUCLEATUM IMPX GENE
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)

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Non-polymers , 4 types, 17 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GZG / 4-{benzyl[2-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)ethyl]amino}butanoic acid


Mass: 461.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H27N5O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 293.15 K / Method: evaporation / pH: 6.5 / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: May 31, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 8864 / % possible obs: 83.4 % / Observed criterion σ(I): 0.5 / Redundancy: 7.1 % / Biso Wilson estimate: 16.83 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.14
Reflection shellResolution: 2.8→3.23 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 2.52 / % possible all: 54.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F4E

3f4e


Resolution: 2.88→19.55 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.854 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.433
RfactorNum. reflection% reflectionSelection details
Rfree0.257 401 4.82 %RANDOM
Rwork0.199 ---
obs0.202 8313 85.2 %-
Displacement parametersBiso max: 190.88 Å2 / Biso mean: 76.52 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--7.2579 Å20 Å20 Å2
2---7.2579 Å20 Å2
3---14.5159 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 2.88→19.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2333 41 9 2383
Biso mean--42.25 12.97 -
Num. residues----109
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d544SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes144HARMONIC5
X-RAY DIFFRACTIONt_it2649HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
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_contact2738SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2649HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4123HARMONIC20.71
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion23.82
LS refinement shellResolution: 2.88→3.22 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.339 102 5.95 %
Rwork0.304 1611 -
all-1713 -
obs--62.35 %
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)
14.49830.3755-1.08692.2960.74063.07790.14370.1286-0.561-0.19740.0165-0.3257-0.24280.0024-0.1602-0.27910.0276-0.0457-0.1638-0.02450.2498.8277-20.99848.1085
25.66231.18730.23214.12581.2742.1560.20420.1994-0.5101-0.56660.0127-0.3431-0.43690.1501-0.217-0.2565-0.03550.0246-0.20230.10310.067912.5496-17.62796.5081
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ X|* }X1 - 53
2X-RAY DIFFRACTION2{ Y|* }Y57 - 112

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