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- PDB-6dn3: CRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1555 SPLIT RNA -

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Basic information

Entry
Database: PDB / ID: 6dn3
TitleCRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1555 SPLIT RNA
Components
  • RNA (56-MER)
  • RNA RIBOSWITCH
KeywordsRNA / FMN / RIBOSWITCH / TRANSCRIPTION
Function / homologyChem-GZ4 / : / RNA / RNA (> 10)
Function and homology information
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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)36,15412
Polymers35,5482
Non-polymers60610
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-70 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.550, 71.550, 140.270
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 , 5 types, 14 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GZ4 / 7,8-dimethyl-2,4-dioxo-10-(3-phenylpropyl)-1,2,3,4-tetrahydrobenzo[g]pteridin-10-ium


Mass: 361.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21N4O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.92 Å3/Da / Density % sol: 57.81 %
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: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 10406 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 61.65 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 24.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 2.3 / % possible all: 87

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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: 2.8→23.1 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.92 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.32 / SU Rfree Cruickshank DPI: 0.302
RfactorNum. reflection% reflectionSelection details
Rfree0.229 501 4.82 %RANDOM
Rwork0.193 ---
obs0.194 10388 96.9 %-
Displacement parametersBiso max: 147.87 Å2 / Biso mean: 81.86 Å2 / Biso min: 45.24 Å2
Baniso -1Baniso -2Baniso -3
1-1.4618 Å20 Å20 Å2
2--1.4618 Å20 Å2
3----2.9237 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: final / Resolution: 2.8→23.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2337 57 4 2398
Biso mean--60.1 59.58 -
Num. residues----110
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d550SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes149HARMONIC5
X-RAY DIFFRACTIONt_it2667HARMONIC20
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_contact2682SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2667HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4166HARMONIC20.74
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion23.06
LS refinement shellResolution: 2.8→3.13 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.282 145 5.25 %
Rwork0.249 2619 -
all-2764 -
obs--92.34 %

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