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- PDB-7tzu: Crystal structure of the E. coli thiM riboswitch bound to 1-(4-(p... -

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Entry
Database: PDB / ID: 7tzu
TitleCrystal structure of the E. coli thiM riboswitch bound to 1-(4-(piperazin-1-yl)pyridin-3-yl)-N-(quinoxalin-6-ylmethyl)methanamine (linked compound 38)
ComponentsRNA (79-MER)
KeywordsRNA / thiM TPP riboswitch
Function / homologyChem-KWL / : / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 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
A: RNA (79-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4028
Polymers26,7991
Non-polymers6037
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.702, 61.702, 102.789
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
Components on special symmetry positions
IDModelComponents
11A-102-

MG

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Components

#1: RNA chain RNA (79-MER)


Mass: 26798.936 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: Chemical ChemComp-KWL / 1-[4-(piperazin-1-yl)pyridin-3-yl]-N-[(quinoxalin-6-yl)methyl]methanamine


Mass: 334.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.11 Å3/Da / Density % sol: 41.64 % / Description: Thick trigonal rod crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: The 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 0.7 mM compound 39. Reservoir solution was 50 mM Bis- ...Details: The 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 0.7 mM compound 39. Reservoir solution was 50 mM Bis-Tris, pH 6.5, 0.45 M ammonium chloride, 10 mm MnCl2, and 30% (w/v) PEG2000
PH range: 6.5-8.0

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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 EIGER2 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: 2.87→30 Å / Num. obs: 5295 / % possible obs: 99.8 % / Redundancy: 11.8 % / Biso Wilson estimate: 84.97 Å2 / CC1/2: 0.944 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.042 / Net I/σ(I): 32
Reflection shellResolution: 2.87→2.92 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.774 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 267 / CC1/2: 0.637 / Rpim(I) all: 0.583 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
HKL-2000data scaling
HKL-2000data reduction
PHASER1.14-3260phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HOJ

2hoj


Resolution: 2.87→29.55 Å / SU ML: 0.3353 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.4753
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2696 1004 10.12 %
Rwork0.2294 8915 -
obs0.2336 5295 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.42 Å2
Refinement stepCycle: LAST / Resolution: 2.87→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1655 31 2 1688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00431879
X-RAY DIFFRACTIONf_angle_d0.74792922
X-RAY DIFFRACTIONf_chiral_restr0.0345390
X-RAY DIFFRACTIONf_plane_restr0.004577
X-RAY DIFFRACTIONf_dihedral_angle_d17.4925946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-3.030.47891420.42611275X-RAY DIFFRACTION98.95
3.03-3.210.31631320.33261287X-RAY DIFFRACTION99.09
3.21-3.460.31211400.26791274X-RAY DIFFRACTION99.16
3.46-3.810.25161420.24511255X-RAY DIFFRACTION98.73
3.81-4.360.25061520.23161269X-RAY DIFFRACTION99.79
4.36-5.490.25391480.21411275X-RAY DIFFRACTION100
5.49-29.550.25491480.18471280X-RAY DIFFRACTION99.58
Refinement TLS params.Method: refined / Origin x: -18.9484504093 Å / Origin y: 1.18030608113 Å / Origin z: -11.8395675547 Å
111213212223313233
T0.768321041532 Å20.214773678269 Å2-0.0335881809519 Å2-0.571793044254 Å2-0.0212802141068 Å2--0.519808391291 Å2
L1.43204546397 °2-1.04230656474 °2-0.210614466639 °2-1.59133684968 °20.405052913635 °2--1.99789283392 °2
S0.382279969227 Å °0.702163903828 Å °-0.189173711113 Å °-0.710482343216 Å °-0.502008496433 Å °0.305509671356 Å °-0.367318063961 Å °0.0588651322865 Å °-0.00962728277763 Å °
Refinement TLS groupSelection details: all

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