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

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Basic information

Entry
Database: PDB / ID: 7tzt
TitleCrystal structure of the E. coli thiM riboswitch in complex with N1,N1-dimethyl-N2-(quinoxalin-6-ylmethyl)ethane-1,2-diamine (linked compound 37)
ComponentsRNA (79-MER)
KeywordsRNA / thiM TPP riboswitch
Function / homology6-methylquinoxaline / : / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 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)27,1635
Polymers26,7991
Non-polymers3644
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.018, 61.018, 102.855
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 RNA (79-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.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-KXC / 6-methylquinoxaline


Mass: 230.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18N4 / Feature type: SUBJECT OF INVESTIGATION
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: 2.06 Å3/Da / Density % sol: 40.36 % / Description: large trigonal shaped 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 1.0 mM compound 38. 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 1.0 mM compound 38. Reservoir solution was 50 mM Bis-Tris, pH 6.5, 0.5 M ammonium chloride, 15 mm MnCl2, and 28% (v/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: 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: 2.93→50 Å / Num. obs: 4715 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 97.5 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.044 / Net I/σ(I): 304.8
Reflection shellResolution: 2.93→2.98 Å / Redundancy: 10.6 % / Rmerge(I) obs: 3.612 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 238 / CC1/2: 0.637 / Rpim(I) all: 1.14 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
HKL-2000data scaling
HKL-2000data reduction
PHASER1.14_3260phasing
Coot0.8.9.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HOJ

2hoj


Resolution: 2.96→47 Å / SU ML: 0.3197 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.9635
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.257 4715 9.93 %
Rwork0.2434 7902 -
obs0.2445 4715 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 115.66 Å2
Refinement stepCycle: LAST / Resolution: 2.96→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1655 14 0 1669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021863
X-RAY DIFFRACTIONf_angle_d0.60462901
X-RAY DIFFRACTIONf_chiral_restr0.0326390
X-RAY DIFFRACTIONf_plane_restr0.004876
X-RAY DIFFRACTIONf_dihedral_angle_d16.6256935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.96-3.150.45971370.39181265X-RAY DIFFRACTION93.97
3.15-3.390.39021500.32151338X-RAY DIFFRACTION98.61
3.39-3.730.26641430.29141299X-RAY DIFFRACTION97.9
3.73-4.270.30051520.26041315X-RAY DIFFRACTION99.12
4.27-5.380.25151560.23821328X-RAY DIFFRACTION100
5.38-470.20741330.2031357X-RAY DIFFRACTION99.53
Refinement TLS params.Method: refined / Origin x: -8.30212374089 Å / Origin y: 16.841211741 Å / Origin z: 5.43754207531 Å
111213212223313233
T0.685663005776 Å2-0.412798219492 Å2-0.0649324666564 Å2-0.00529678218144 Å20.0520193013509 Å2--0.251497051157 Å2
L0.136576582032 °20.129360935303 °20.0255139561372 °2-0.203406248141 °2-0.044277780593 °2--0.132181880406 °2
S0.0658325078211 Å °0.0817506027434 Å °0.252618332053 Å °-0.868636280827 Å °-0.0122083471605 Å °0.42858067413 Å °0.139212427147 Å °0.46613622091 Å °-2.17129811337E-9 Å °
Refinement TLS groupSelection details: all

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