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- PDB-7tzr: Crystal structure of the E. coli thiM riboswitch bound to N-methy... -

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Basic information

Entry
Database: PDB / ID: 7tzr
TitleCrystal structure of the E. coli thiM riboswitch bound to N-methyl-1-(quinoxalin-6-yl)methanamine (compound 16)
ComponentsRNA (80-MER)
KeywordsRNA / thiM TPP riboswitch
Function / homology: / N-methyl-1-(quinoxalin-6-yl)methanamine / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: SHAPE-enabled fragment-based ligand discovery for RNA.
Authors: Zeller, M.J. / Favorov, O. / Li, K. / Nuthanakanti, A. / Hussein, D. / Michaud, A. / Lafontaine, D.A. / Busan, S. / Serganov, A. / Aube, J. / Weeks, K.M.
History
DepositionFeb 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: RNA (80-MER)
Y: RNA (80-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5177
Polymers52,0842
Non-polymers4335
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.156, 29.608, 95.507
Angle α, β, γ (deg.)90.000, 94.321, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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RNA chain , 1 types, 2 molecules XY

#1: RNA chain RNA (80-MER)


Mass: 26042.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 5 types, 39 molecules

#2: Chemical ChemComp-KWU / N-methyl-1-(quinoxalin-6-yl)methanamine


Mass: 173.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.03 Å3/Da / Density % sol: 39.48 % / Description: shapeless rod cluster
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: TPP riboswitch RNA (0.2 mM) and 16 (2 mM) were heated in a buffer containing 50 mM potassium acetate (pH 6.8) and 3 (compound 16) mM MgCl2. Reservoir solution containing 0.1 M sodium acetate ...Details: TPP riboswitch RNA (0.2 mM) and 16 (2 mM) were heated in a buffer containing 50 mM potassium acetate (pH 6.8) and 3 (compound 16) mM MgCl2. Reservoir solution containing 0.1 M sodium acetate (pH 4.8), 0.35 M ammonium acetate, and 28% (v/v) PEG4000
PH range: 4.8-6.8

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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: 0.9252 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9252 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 11400 / % possible obs: 95.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 42.65 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.101 / Net I/σ(I): 9.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1061 / CC1/2: 0.656 / Rpim(I) all: 0.407 / % possible all: 92.3

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GDI

2gdi


Resolution: 2.7→29.05 Å / SU ML: 0.4157 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.9874
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2609 1153 10.13 %
Rwork0.2036 10229 -
obs0.2095 11382 94.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.91 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3399 29 34 3462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323826
X-RAY DIFFRACTIONf_angle_d0.84755962
X-RAY DIFFRACTIONf_chiral_restr0.039786
X-RAY DIFFRACTIONf_plane_restr0.0057159
X-RAY DIFFRACTIONf_dihedral_angle_d18.84321931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.820.38881280.32351154X-RAY DIFFRACTION87.57
2.82-2.970.35331450.27961292X-RAY DIFFRACTION95.61
2.97-3.150.34311380.25281255X-RAY DIFFRACTION96.53
3.15-3.40.30181510.21471316X-RAY DIFFRACTION97.15
3.4-3.740.25811490.20861310X-RAY DIFFRACTION97.07
3.74-4.280.24781500.17981302X-RAY DIFFRACTION96.93
4.28-5.380.22911480.17131294X-RAY DIFFRACTION94.62
5.39-29.050.18861440.16661306X-RAY DIFFRACTION90.51

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