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- PDB-3f4g: Crystal structure of the FMN riboswitch bound to riboflavin. -

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Basic information

Entry
Database: PDB / ID: 3f4g
TitleCrystal structure of the FMN riboswitch bound to riboflavin.
Components(FMN riboswitch) x 2
KeywordsRNA / riboflavin / FMN / riboswitch / transcription
Function / homology: / RIBOFLAVIN / : / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 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)36,36720
Polymers35,5482
Non-polymers81918
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.203, 71.203, 137.711
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 / 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
#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.: 15 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2


Mass: 376.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N4O6

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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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 0.1 M Tris-HCl pH 8.4 10% PEG 4000 0.2 M MgCl2, 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: 8473 / Num. obs: 8439 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 58.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 15.4 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 6 / Num. unique all: 829 / % possible all: 100

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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: 3.01→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / SU B: 45.153 / SU ML: 0.378 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.447 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26325 384 4.7 %RANDOM
Rwork0.20634 ---
all0.20876 8069 --
obs0.20876 7850 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.201 Å2
Baniso -1Baniso -2Baniso -3
1-2.65 Å21.32 Å20 Å2
2--2.65 Å20 Å2
3----3.97 Å2
Refine analyzeLuzzati coordinate error obs: 0.388 Å
Refinement stepCycle: LAST / Resolution: 3.01→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2340 44 0 2384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212648
X-RAY DIFFRACTIONr_angle_refined_deg1.02334125
X-RAY DIFFRACTIONr_chiral_restr0.050.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021159
X-RAY DIFFRACTIONr_nbd_refined0.170.21078
X-RAY DIFFRACTIONr_nbtor_refined0.2790.21653
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.261
X-RAY DIFFRACTIONr_metal_ion_refined0.0290.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.215
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.21
X-RAY DIFFRACTIONr_scbond_it0.65532825
X-RAY DIFFRACTIONr_scangle_it1.0494.54125
LS refinement shellResolution: 3.01→3.081 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 24 -
Rwork0.312 576 -
obs-600 97.24 %
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)
132.30465.7648-14.433816.0774-2.065618.9843-1.4117-1.2914-2.7606-0.26640.19141.42760.7683-1.31231.22030.20810.2276-0.46780.80680.15621.10972.65427.20614.692
22.8697-0.29910.66683.14090.69276.20170.26580.0586-0.15480.1464-0.1445-0.086-0.08210.4663-0.1213-0.2716-0.00460.0035-0.0849-0.07140.221944.76842.3079.278
35.14750.45612.07112.59670.11583.98480.0344-0.4018-0.22380.83480.18740.17240.2351-0.738-0.2218-0.18380.01340.0708-0.13130.03630.217517.32747.1317.619
411.9786-1.933.546415.8228.54929.0154-0.5877-1.20190.22641.94110.01040.9701-1.11641.00520.57720.6586-0.3135-0.04310.1740.40010.592222.69133.66235.553
57.8377-1.92022.78825.0463-0.69733.2746-0.4273-0.33130.61580.65320.36330.2219-0.7959-0.20040.064-0.08210.04370.0887-0.1599-0.05250.206922.26559.90314.91
67.568-0.6485-0.1952.20760.18511.75990.32920.0827-1.98860.0607-0.07250.53010.3089-0.5824-0.2567-0.1529-0.047-0.04720.00640.06410.600323.83930.85716.104
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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