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- PDB-7mlw: Burkholderia sp. TJI49 Guanidine-I riboswitch -

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Basic information

Entry
Database: PDB / ID: 7mlw
TitleBurkholderia sp. TJI49 Guanidine-I riboswitch
ComponentsGuanidine-I riboswitch
KeywordsRNA / Riboswitch / guanidine / potassium / ion / A-minor
Function / homologyGUANIDINE / : / PHOSPHATE ION / STRONTIUM ION / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesBurkholderia sp. TJI49 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTrachman, R.J. / Ferre-D'Amare, A.R.
CitationJournal: Rna / Year: 2021
Title: An uncommon [K + (Mg 2+ ) 2 ] metal ion triad imparts stability and selectivity to the Guanidine-I riboswitch.
Authors: Trachman 3rd, R.J. / Ferre-D'Amare, A.R.
History
DepositionApr 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 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
F: Guanidine-I riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,27014
Polymers41,4661
Non-polymers80413
Water23413
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.703, 51.703, 266.728
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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RNA chain , 1 types, 1 molecules F

#1: RNA chain Guanidine-I riboswitch


Mass: 41465.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia sp. TJI49 (bacteria)
Production host: in vitro transcription vector pT7-TP(deltai) (others)

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Non-polymers , 6 types, 26 molecules

#2: Chemical ChemComp-GAI / GUANIDINE / Guanidine


Mass: 59.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: CH5N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 mM HEPES (pH 7.5), 200 mM ammonium sulfate, 10 mM strontium chloride, 30% PEG 3350, 3% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9919 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 2.7→7 Å / Num. obs: 11350 / % possible obs: 98 % / Redundancy: 18.2 % / Biso Wilson estimate: 67.71 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.7
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 18.2 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 936 / CC1/2: 0.92 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T83

5t83


Resolution: 2.7→6.99 Å / SU ML: 0.3528 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.8037
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2703 1143 10.07 %
Rwork0.2181 10207 -
obs0.2232 11350 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.08 Å2
Refinement stepCycle: LAST / Resolution: 2.7→6.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2680 32 13 2725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00563039
X-RAY DIFFRACTIONf_angle_d1.15494732
X-RAY DIFFRACTIONf_chiral_restr0.0488629
X-RAY DIFFRACTIONf_plane_restr0.0079127
X-RAY DIFFRACTIONf_dihedral_angle_d17.30841499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.820.37311400.34831241X-RAY DIFFRACTION100
2.82-2.950.35271380.30581243X-RAY DIFFRACTION99.93
2.95-3.120.26451430.2891256X-RAY DIFFRACTION99.43
3.12-3.340.28541370.21731256X-RAY DIFFRACTION99.15
3.34-3.630.27321440.22781272X-RAY DIFFRACTION99.51
3.63-4.060.24011430.20341293X-RAY DIFFRACTION99.79
4.07-4.820.24571480.20011297X-RAY DIFFRACTION100
4.82-6.990.27041500.18281349X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -13.8534670905 Å / Origin y: 3.73034604913 Å / Origin z: -18.2165343402 Å
111213212223313233
T0.509819820509 Å2-0.0443216223163 Å2-0.0981496360206 Å2-0.849977218286 Å20.073044706201 Å2--0.417252805292 Å2
L1.26654887555 °20.29059107518 °20.190243280122 °2-1.02776674007 °20.640861134726 °2--3.23098813948 °2
S-0.0534112445843 Å °0.242455832669 Å °0.0717136406825 Å °-0.13831231811 Å °0.313241710716 Å °0.207410270496 Å °-0.116994830733 Å °-1.338783507 Å °-0.0923387249597 Å °
Refinement TLS groupSelection details: all

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