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- PDB-3f30: Crystal structure of the FMN riboswitch bound to FMN, cobalt hexa... -

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Basic information

Entry
Database: PDB / ID: 3f30
TitleCrystal structure of the FMN riboswitch bound to FMN, cobalt hexammine soak.
ComponentsFMN riboswitch
KeywordsRNA / FMN / riboswitch / transcription / cobalt hexamine
Function / homologyFLAVIN MONONUCLEOTIDE / : / COBALT HEXAMMINE(III) / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 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

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Assembly

Deposited unit
X: FMN riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,59120
Polymers36,4511
Non-polymers2,14019
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.156, 71.156, 138.421
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 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CoH18N6

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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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 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: NSLS / Beamline: X29A / Wavelength: 1.606041 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: 1.606041 Å / Relative weight: 1
ReflectionResolution: 3.15→20 Å / Num. all: 7467 / Num. obs: 7437 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 39.4
Reflection shellResolution: 3.15→3.26 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 6.9 / Num. unique all: 736 / % possible all: 96.9

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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: 3F2Q

3f2q


Resolution: 3.15→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.933 / SU B: 43.621 / SU ML: 0.368 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23442 334 4.5 %RANDOM
Rwork0.18499 ---
all0.18718 7069 --
obs0.18718 7037 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.282 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.12 Å20 Å2
2--0.23 Å20 Å2
3----0.35 Å2
Refine analyzeLuzzati coordinate error obs: 0.368 Å
Refinement stepCycle: LAST / Resolution: 3.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2353 103 0 2456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212726
X-RAY DIFFRACTIONr_angle_refined_deg1.03634290
X-RAY DIFFRACTIONr_chiral_restr0.050.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021164
X-RAY DIFFRACTIONr_nbd_refined0.1570.21086
X-RAY DIFFRACTIONr_nbtor_refined0.2760.21636
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.289
X-RAY DIFFRACTIONr_metal_ion_refined0.0260.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.21
X-RAY DIFFRACTIONr_scbond_it0.53332905
X-RAY DIFFRACTIONr_scangle_it0.8674.54290
LS refinement shellResolution: 3.15→3.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 29 -
Rwork0.292 484 -
obs-513 95.71 %
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)
122.898413.6136-13.25399.103-9.17619.3365-1.5072-2.0424-1.85940.56091.3046-0.0137-0.11120.13440.2026-0.10160.1313-0.05971.09390.01961.43652.65427.20614.692
26.5062-1.5694-3.34991.3303-0.41094.6691-0.02250.29-0.0866-0.02990.0354-0.0903-0.08490.8545-0.0129-0.3715-0.0669-0.04380.1658-0.07620.248744.76842.3079.278
37.0246-1.57640.80164.9872-1.73541.69570.1507-0.5859-0.22930.5136-0.00990.5207-0.3267-0.2865-0.1408-0.26040.03080.0791-0.1923-0.03490.180917.32747.1317.619
410.09721.6811-5.724315.504610.821512.3514-0.1323-1.4456-0.75952.6165-0.64412.34230.57470.22460.77640.79160.04780.11960.23390.44280.584122.69133.66235.553
57.4378-2.79582.36248.5157-0.27573.851-0.4034-0.14360.67790.9330.16190.6303-1.0883-0.1960.24150.04040.04640.0806-0.2469-0.09060.176522.26559.90314.91
611.4604-1.1050.83461.53530.01513.03350.018-0.0234-2.46830.01980.08660.52390.4231-0.3409-0.1046-0.230.01270.0619-0.03350.02920.654323.83930.85716.104
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 DIFFRACTION4X49 - 60
5X-RAY DIFFRACTION5X61 - 84
6X-RAY DIFFRACTION6X85 - 112

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