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- PDB-7kd1: Apo structure of the THF riboswitch aptamer domain -

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Basic information

Entry
Database: PDB / ID: 7kd1
TitleApo structure of the THF riboswitch aptamer domain
Componentstetrahydrofolate riboswitch aptamer domain
KeywordsRNA / riboswitch / apo / gene regulation
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesStreptococcus mutans UA159 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWilt, H.M. / Stagno, J.R. / Wang, Y.-X.
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation.
Authors: Wilt, H.M. / Yu, P. / Tan, K. / Wang, Y.X. / Stagno, J.R.
History
DepositionOct 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 18, 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

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Assembly

Deposited unit
A: tetrahydrofolate riboswitch aptamer domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0664
Polymers28,8491
Non-polymers2163
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.040, 74.040, 122.260
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-206-

HOH

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Components

#1: RNA chain tetrahydrofolate riboswitch aptamer domain


Mass: 28849.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus mutans UA159 (bacteria)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 100 mM MES, pH 5.6, 200 mM NaCl, 2.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→40.75 Å / Num. obs: 30818 / % possible obs: 98.73 % / Redundancy: 7.34 % / CC1/2: 1 / Rmerge(I) obs: 0.026 / Rpim(I) all: 0.01 / Rrim(I) all: 0.028 / Net I/σ(I): 29.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.07 % / Rmerge(I) obs: 3.639 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2962 / CC1/2: 0.488 / Rpim(I) all: 1.6 / Rrim(I) all: 3.985 / % possible all: 97.21

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Processing

Software
NameVersionClassification
PHENIXdev-3900refinement
XSCALE20200131data scaling
PDB_EXTRACT3.25data extraction
XDS20200131data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LVV

4lvv


Resolution: 1.9→40.75 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2255 1579 5.16 %
Rwork0.2048 29038 -
obs0.2059 30617 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 216.86 Å2 / Biso mean: 87.75 Å2 / Biso min: 43.89 Å2
Refinement stepCycle: final / Resolution: 1.9→40.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1914 11 27 1952
Biso mean--73.88 63.04 -
Num. residues----89
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.970.47441420.44942634277691
1.97-2.050.45161500.44442871302198
2.05-2.140.41371730.38452841301498
2.14-2.250.38921290.3412906303599
2.25-2.390.31381680.30182912308099
2.39-2.580.32321520.30212914306699
2.58-2.840.36321470.316329613108100
2.84-3.250.28921620.24812948311099
3.25-4.090.18621700.1792983315399
4.09-40.750.17491860.15153068325498
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)
10.3146-1.1628-0.94681.4663.2791.4988-0.2232-0.18830.25240.72690.2734-0.19540.54190.3143-0.18351.11420.20940.02810.7494-0.12110.825422.829742.708892.0426
21.19380.6881-0.13842.4408-1.59892.1659-0.0939-0.1578-0.3739-0.00420.1575-0.20570.4561-0.2933-0.02520.71550.03370.04460.58280.07410.643218.204221.683377.6655
30.0588-0.7242-0.58643.8852.69851.67360.4514-0.25280.62781.5118-0.52610.9246-0.6164-0.91140.02261.92850.34650.29431.0171-0.10641.011412.047130.3639104.7161
40.0104-0.0524-0.3430.8233-0.57782.00880.00580.088-0.09340.04490.1931-0.11640.33080.0865-0.1240.58350.06670.02150.5872-0.00690.567224.122227.726370.1689
5-0.6074-0.1154-0.38161.03373.59743.0085-0.1629-0.1620.21790.57450.0559-0.07730.2647-0.1262-0.11851.2310.2548-0.00290.9091-0.17030.749419.532843.55998.1088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )A1 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 30 )A21 - 30
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 45 )A31 - 45
4X-RAY DIFFRACTION4chain 'A' and (resid 46 through 65 )A46 - 65
5X-RAY DIFFRACTION5chain 'A' and (resid 66 through 89 )A66 - 89

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