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- PDB-3f2x: Crystal structure of the FMN riboswitch bound to FMN, Cs+ soak. -

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Basic information

Entry
Database: PDB / ID: 3f2x
TitleCrystal structure of the FMN riboswitch bound to FMN, Cs+ soak.
ComponentsFMN riboswitch
KeywordsRNA / FMN / riboswitch / transcription / cesium
Function / homology: / FLAVIN MONONUCLEOTIDE / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 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 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: FMN riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,75519
Polymers36,4511
Non-polymers1,30418
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.370, 71.370, 140.938
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: 36451.418 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: In vitro transcribed RNA from the Fusobacterium nucleatum impX gene
References: GenBank: 20095250
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cs
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES-Na pH 6.5 10% PEG 4000 0.1 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES-Na11
2PEG400011
3MgCl211
4MES-Na12
5PEG400012
6MgCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.493786 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.493786 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. all: 8321 / Num. obs: 7822 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 47.3
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2.9 / Num. unique all: 776 / % possible all: 94.3

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F2Q

3f2q


Resolution: 3.11→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 39.329 / SU ML: 0.326 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21456 355 4.6 %RANDOM
Rwork0.19229 ---
all0.19332 7482 --
obs0.19332 7336 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 98.423 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å2-0.59 Å20 Å2
2---1.18 Å20 Å2
3---1.76 Å2
Refine analyzeLuzzati coordinate error obs: 0.326 Å
Refinement stepCycle: LAST / Resolution: 3.11→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2353 48 2 2403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0212670
X-RAY DIFFRACTIONr_angle_refined_deg1.05834155
X-RAY DIFFRACTIONr_chiral_restr0.0490.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021164
X-RAY DIFFRACTIONr_nbd_refined0.1460.2858
X-RAY DIFFRACTIONr_nbtor_refined0.2710.21605
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.265
X-RAY DIFFRACTIONr_metal_ion_refined0.0340.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1120.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0050.21
X-RAY DIFFRACTIONr_scbond_it0.43332769
X-RAY DIFFRACTIONr_scangle_it0.7284.54155
LS refinement shellResolution: 3.11→3.194 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.477 18 -
Rwork0.383 489 -
obs-507 90.86 %
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)
112.50571.16550.27032.22080.42542.00310.1343-0.2376-2.1828-0.1943-0.04930.73620.2766-0.8325-0.085-0.2072-0.06610.00480.16450.12070.496118.752630.19815.6094
28.53910.1346-1.77863.6721-1.07167.76760.18860.2969-0.35710.0614-0.2417-0.09-0.2910.91050.0532-0.3853-0.05730.0434-0.0767-0.1109-0.264445.1542.57579.2248
34.2757-0.377-0.0085.8024-2.19311.6893-0.1089-0.6014-0.57480.90150.20020.4956-0.4162-0.75-0.0913-0.17050.15370.14470.01840.0189-0.171917.47247.537717.6537
411.35455.3661-7.72896.0296-0.97087.46130.1677-2.0209-1.10112.244-1.85611.9066-1.67980.94521.68840.9254-0.11940.02810.47130.51670.398522.338833.826435.4522
510.4165-4.76994.35138.4348-2.34174.0807-0.7476-0.84980.6821.07280.52920.2567-1.4491-0.5260.21840.11060.16660.1379-0.1329-0.1726-0.227922.47160.401414.9466
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X1 - 9
2X-RAY DIFFRACTION1X85 - 112
3X-RAY DIFFRACTION2X10 - 30
4X-RAY DIFFRACTION3X31 - 48
5X-RAY DIFFRACTION4X49 - 60
6X-RAY DIFFRACTION5X61 - 84

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