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- PDB-6hbt: The structure of the G. violaceus guanidine II riboswitch P2 stem... -

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Basic information

Entry
Database: PDB / ID: 6hbt
TitleThe structure of the G. violaceus guanidine II riboswitch P2 stem-loop with arcaine
ComponentsRNA (5'-R(*GP*GP*UP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*AP*(CBV)P*C)-3')
KeywordsRNA / guanidine II riboswitch / stem-loop / tetra loop / dimer
Function / homology1-(4-carbamimidamidobutyl)guanidine / RNA / RNA (> 10)
Function and homology information
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.66 Å
AuthorsHuang, L. / Lilley, D.M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKA18604 United Kingdom
CitationJournal: Rna / Year: 2019
Title: Structure-guided design of a high-affinity ligand for a riboswitch.
Authors: Huang, L. / Wang, J. / Wilson, T.J. / Lilley, D.M.J.
History
DepositionAug 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_assembly ...diffrn_source / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly.details ..._diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Apr 3, 2019Group: Atomic model / Data collection / Category: atom_site
Revision 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*UP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*AP*(CBV)P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2454
Polymers5,8801
Non-polymers3643
Water72140
1
A: RNA (5'-R(*GP*GP*UP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*AP*(CBV)P*C)-3')
hetero molecules

A: RNA (5'-R(*GP*GP*UP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*AP*(CBV)P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4908
Polymers11,7612
Non-polymers7296
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Unit cell
Length a, b, c (Å)55.460, 55.460, 135.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-215-

HOH

21A-217-

HOH

31A-220-

HOH

41A-222-

HOH

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Components

#1: RNA chain RNA (5'-R(*GP*GP*UP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*AP*(CBV)P*C)-3')


Mass: 5880.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Gloeobacter violaceus (bacteria)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FXQ / 1-(4-carbamimidamidobutyl)guanidine


Mass: 172.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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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: 3.4 Å3/Da / Density % sol: 63.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.01 M Magnesium Acetate, 0.05 M MES pH 5.6, 2.5 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9197 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9197 Å / Relative weight: 1
ReflectionResolution: 1.66→27.73 Å / Num. obs: 17902 / % possible obs: 98.88 % / Observed criterion σ(I): 1.3 / Redundancy: 4.79 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.028 / Net I/σ(I): 19.6
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 5 % / Rmerge(I) obs: 1.316 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 463 / CC1/2: 0.571 / Rpim(I) all: 0.647 / % possible all: 97.06

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Processing

Software
NameVersionClassification
PHENIX(1.14_3228: ???)refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.66→27.73 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.11
RfactorNum. reflection% reflection
Rfree0.2138 821 4.59 %
Rwork0.2062 --
obs0.2066 17902 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.66→27.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 385 22 40 447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008449
X-RAY DIFFRACTIONf_angle_d1.195694
X-RAY DIFFRACTIONf_dihedral_angle_d13.29211
X-RAY DIFFRACTIONf_chiral_restr0.05588
X-RAY DIFFRACTIONf_plane_restr0.00918
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6601-1.7640.3536970.30822865X-RAY DIFFRACTION97
1.764-1.90020.29031880.27862807X-RAY DIFFRACTION98
1.9002-2.09140.25931100.24292859X-RAY DIFFRACTION98
2.0914-2.39390.25061450.2212896X-RAY DIFFRACTION99
2.3939-3.01540.17471420.23082846X-RAY DIFFRACTION98
3.0154-27.73390.20191390.17142808X-RAY DIFFRACTION96

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