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- PDB-7td7: Crystal structure of an E. coli thiM riboswitch bound to thiamine... -

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Basic information

Entry
Database: PDB / ID: 7td7
TitleCrystal structure of an E. coli thiM riboswitch bound to thiamine, manganese ions
ComponentsthiM riboswitch RNA (78-MER)
KeywordsRNA
Function / homology: / Chem-VIB / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsNuthanakanti, A. / Serganov, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM112940 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 (78-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1685
Polymers26,7991
Non-polymers3694
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.110, 61.110, 103.416
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Space group name HallP322(x,y,z+1/6)
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 (78-MER)


Mass: 26798.936 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-VIB / 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM / THIAMIN / VITAMIN B1


Mass: 265.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N4OS / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
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: 2.08 Å3/Da / Density % sol: 40.87 % / Description: Rod-shaped crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
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 1.0 mM of thiamine. the reservoir solution was 50 mM Bis- ...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 1.0 mM of thiamine. the reservoir solution was 50 mM Bis-Tris HCl, pH 6.5, 0.5 M NH4Cl, 10 mm MnCl2, and 30% (v/v) PEG2000
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.95→30 Å / Num. obs: 4766 / % possible obs: 98.8 % / Redundancy: 8.4 % / Biso Wilson estimate: 89.44 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.043 / Net I/σ(I): 47.6
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 445 / CC1/2: 0.933 / Rpim(I) all: 0.237 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER1.14_3260phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HOJ

2hoj


Resolution: 2.95→29.3 Å / SU ML: 0.3703 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 41.5488
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2856 857 9.81 %
Rwork0.2296 7875 -
obs0.2353 4766 96.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 110 Å2
Refinement stepCycle: LAST / Resolution: 2.95→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1594 21 0 1615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511800
X-RAY DIFFRACTIONf_angle_d1.07562799
X-RAY DIFFRACTIONf_chiral_restr0.0515369
X-RAY DIFFRACTIONf_plane_restr0.007475
X-RAY DIFFRACTIONf_dihedral_angle_d16.5773888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.140.421240.32351195X-RAY DIFFRACTION88.05
3.14-3.380.28291520.27691325X-RAY DIFFRACTION97.81
3.38-3.720.34211440.20921328X-RAY DIFFRACTION97.74
3.72-4.260.24921460.2681348X-RAY DIFFRACTION98.42
4.26-5.360.25041470.24621338X-RAY DIFFRACTION98.61
5.37-29.30.29261440.19421341X-RAY DIFFRACTION97.76
Refinement TLS params.Method: refined / Origin x: 10.6305134248 Å / Origin y: 19.5574279931 Å / Origin z: -5.61707477954 Å
111213212223313233
T0.541219629849 Å20.106742539844 Å2-0.0185633808709 Å2-1.01212353254 Å2-0.00401698921629 Å2--0.636771232433 Å2
L2.96648363931 °2-0.232260240671 °20.312430883359 °2-1.36921220898 °2-0.474667000177 °2--1.88117881239 °2
S-0.199651439037 Å °-1.03422595504 Å °-0.238701582226 Å °0.330842753436 Å °0.261783459901 Å °0.000488857121416 Å °-0.15103974695 Å °0.0745204598246 Å °0.000769678122241 Å °
Refinement TLS groupSelection details: all

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