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- PDB-3f4h: Crystal structure of the FMN riboswitch bound to roseoflavin -

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Basic information

Entry
Database: PDB / ID: 3f4h
TitleCrystal structure of the FMN riboswitch bound to roseoflavin
Components(FMN riboswitch) x 2
KeywordsRNA / Roseoflavin / FMN / riboswitch / transcription
Function / homology: / Chem-RS3 / : / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSerganov, A.A. / Huang, L.
CitationJournal: Nature / Year: 2009
Title: Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch.
Authors: Serganov, A. / Huang, L. / Patel, D.J.
History
DepositionOct 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 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)36,29916
Polymers35,5482
Non-polymers75114
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.726, 70.726, 135.575
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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 FMN riboswitch


Mass: 17455.389 Da / Num. of mol.: 1 / Mutation: U52C,A53U / Source method: obtained synthetically
Details: In vitro transcribed RNA from the Fusobacterium nucleatum impX gene
References: GenBank: 20095250
#2: RNA chain FMN riboswitch


Mass: 18092.771 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: In vitro transcribed RNA from the Fusobacterium nucleatum impX gene
References: GenBank: 20095250

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Non-polymers , 4 types, 15 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-RS3 / 1-deoxy-1-[8-(dimethylamino)-7-methyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl]-D-ribitol / Roseoflavin


Mass: 405.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H23N5O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 0.1 M Tris-HCl 8% PEG4000 0.2 M MgCl2, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris-HCL11
2PEG400011
3MgCl211
4Tris-HCL12
5PEG400012
6MgCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 8679 / Num. obs: 8332 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 56
Reflection shellResolution: 3→3.11 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 4.7 / Num. unique all: 819 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CBASSdata collection
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F4E

3f4e


Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.96 / SU B: 44.683 / SU ML: 0.371 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22836 373 4.5 %RANDOM
Rwork0.19073 ---
all0.19243 7887 --
obs0.19243 7829 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 97.892 Å2
Baniso -1Baniso -2Baniso -3
1--3.14 Å2-1.57 Å20 Å2
2---3.14 Å20 Å2
3---4.71 Å2
Refine analyzeLuzzati coordinate error obs: 0.371 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2340 42 1 2383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212650
X-RAY DIFFRACTIONr_angle_refined_deg1.01734128
X-RAY DIFFRACTIONr_chiral_restr0.0510.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021161
X-RAY DIFFRACTIONr_nbd_refined0.1790.21058
X-RAY DIFFRACTIONr_nbtor_refined0.2810.21641
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0560.21
X-RAY DIFFRACTIONr_scbond_it0.79532851
X-RAY DIFFRACTIONr_scangle_it1.3214.54128
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 18 -
Rwork0.322 572 -
obs-590 98.33 %
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)
121.78144.8014.853815.3287-6.0813.44-1.5794-1.3466-2.2678-0.70470.85841.42660.2189-0.49490.721-0.09850.3019-0.36950.97530.05211.19352.65427.20614.692
24.34260.86980.69132.31330.97885.13820.18480.0927-0.3388-0.1363-0.1189-0.10160.14840.4469-0.0659-0.48150.02320.08330.0081-0.06210.32344.76842.3079.278
35.78260.09712.87857.1081-1.79054.13930.0858-0.2586-0.36481.00830.31830.5072-0.4706-0.8644-0.4041-0.48890.13220.0683-0.24890.02640.157217.32747.1317.619
414.72622.9002-4.94344.47883.56616.93330.0718-2.18180.45242.2057-0.57181.5041-0.17-0.2620.50.8528-0.0363-0.04810.84560.21570.797322.69133.66235.553
59.2632-2.10922.86439.4403-2.07663.5295-0.499-0.14721.04091.03610.20420.0554-1.09540.03760.2948-0.2880.06120.1068-0.2861-0.06980.135222.26559.90314.91
66.6834-0.3278-1.48861.6959-0.161.33560.45810.5328-1.9674-0.1335-0.19050.43310.466-0.3871-0.2675-0.2816-0.0201-0.0807-0.0838-0.0130.725623.83930.85716.104
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X1 - 9
2X-RAY DIFFRACTION2X10 - 30
3X-RAY DIFFRACTION3X31 - 48
4X-RAY DIFFRACTION4Y57 - 60
5X-RAY DIFFRACTION4X49 - 54
6X-RAY DIFFRACTION5Y61 - 84
7X-RAY DIFFRACTION6Y85 - 112

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