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- PDB-7tdc: Crystal structure of the E. coli thiM riboswitch in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7tdc
TitleCrystal structure of the E. coli thiM riboswitch in complex with thiamine bisphosphonate, calcium ions
ComponentsthiM riboswitch RNA (83-MER)
KeywordsRNA
Function / homologyChem-GMI / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsNuthanakanti, A. / Serganov, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM112940 United States
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery.
Authors: Zeller, M.J. / Nuthanakanti, A. / Li, K. / Aube, J. / Serganov, A. / Weeks, K.M.
History
DepositionDec 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_radiation / pdbx_initial_refinement_model
Item: _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: thiM riboswitch RNA (83-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4227
Polymers26,8611
Non-polymers5616
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.006, 65.006, 101.274
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: -y,-x,-z+1/3
#5: -x+y,y,-z+2/3
#6: x,x-y,-z

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Components

#1: RNA chain thiM riboswitch RNA (83-MER)


Mass: 26860.900 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: Chemical ChemComp-GMI / [2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-5-yl]ethoxy-oxidanyl-phosphoryl]methylphosphonic acid


Mass: 423.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H21N4O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: RNA (0.15 mM) was incubated in a buffer containing 5 mM Tris-HCl, pH 8.0, 3 mM MgCl2, 10 mM NaCl, 0.1 M KCl, and 0.5 mM spermine with 0.75 mM TPPc. Reservoir solution was 50 mM sodium ...Details: RNA (0.15 mM) was incubated in a buffer containing 5 mM Tris-HCl, pH 8.0, 3 mM MgCl2, 10 mM NaCl, 0.1 M KCl, and 0.5 mM spermine with 0.75 mM TPPc. Reservoir solution was 50 mM sodium cacodylate, pH 6.0, 0.3 M NH4Cl, 10 mm CaCl2, and 30% (v/v) PEG2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.46→56.3 Å / Num. obs: 9133 / % possible obs: 99.9 % / Redundancy: 13.8 % / Biso Wilson estimate: 84.79 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.9
Reflection shellResolution: 2.46→2.56 Å / Redundancy: 12.9 % / Rmerge(I) obs: 3.73 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1026 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HOJ

2hoj


Resolution: 2.46→56.3 Å / SU ML: 0.521 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.444
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.247 1681 9.85 %
Rwork0.211 --
obs0.215 9133 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.15 Å2
Refinement stepCycle: LAST / Resolution: 2.46→56.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1664 31 14 1709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051900
X-RAY DIFFRACTIONf_angle_d1.1162951
X-RAY DIFFRACTIONf_dihedral_angle_d18.315938
X-RAY DIFFRACTIONf_chiral_restr0.053384
X-RAY DIFFRACTIONf_plane_restr0.00678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.530.48011070.44941096X-RAY DIFFRACTION83
2.53-2.610.51041460.4541313X-RAY DIFFRACTION99
2.61-2.710.41841460.42851290X-RAY DIFFRACTION100
2.71-2.820.37061390.36491314X-RAY DIFFRACTION100
2.82-2.940.41411300.34341301X-RAY DIFFRACTION100
2.94-3.10.27541540.27491291X-RAY DIFFRACTION100
3.1-3.290.31481430.26641292X-RAY DIFFRACTION99
3.29-3.550.26361480.21111280X-RAY DIFFRACTION99
3.55-3.90.23771450.20141292X-RAY DIFFRACTION99
3.91-4.470.20311450.20841289X-RAY DIFFRACTION100
4.47-5.630.21331400.17961318X-RAY DIFFRACTION100
5.64-56.30.20841380.15811315X-RAY DIFFRACTION100

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