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- PDB-5t83: Structure of a guanidine-I riboswitch from S. acidophilus -

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Basic information

Entry
Database: PDB / ID: 5t83
TitleStructure of a guanidine-I riboswitch from S. acidophilus
ComponentsRNA (95-MER)
KeywordsRNA / riboswitch / guanidine / s-turn / a-minor
Function / homologyGUANIDINE / IRIDIUM HEXAMMINE ION / SPERMINE (FULLY PROTONATED FORM) / STRONTIUM ION / : / RNA / RNA (> 10)
Function and homology information
Biological speciesSulfobacillus acidophilus DSM 10332 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.71 Å
AuthorsReiss, C.W. / Xiong, Y. / Strobel, S.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM022778 United States
Citation
Journal: Structure / Year: 2017
Title: Structural Basis for Ligand Binding to the Guanidine-I Riboswitch.
Authors: Reiss, C.W. / Xiong, Y. / Strobel, S.A.
#1: Journal: to be published
Title: Metabolism of Free Guanidine in Bacteria is Regulated by Widespread Riboswitch Classes
Authors: Nelson, J.W. / Atilho, R.M. / Sherlock, M.E. / Reiss, C.W. / Strobel, S.A. / Stockbridge, R.B. / Breaker, R.R.
History
DepositionSep 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.version
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (95-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,72217
Polymers30,7361
Non-polymers1,98616
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.091, 49.091, 246.341
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain RNA (95-MER)


Mass: 30736.305 Da / Num. of mol.: 1 / Mutation: U24G, A25U, G26C, C30G, U31G, A32U / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription with T7 RNA polymerase
Source: (synth.) Sulfobacillus acidophilus DSM 10332 (bacteria)
References: GenBank: 361052061

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Non-polymers , 6 types, 34 molecules

#2: Chemical
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Sr
#3: Chemical ChemComp-SPK / SPERMINE (FULLY PROTONATED FORM) / Spermine


Mass: 206.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H30N4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H18IrN6
#6: Chemical ChemComp-GAI / GUANIDINE / Guanidine


Mass: 59.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5N3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 296 K / Method: microbatch / pH: 4.6
Details: RNA solution: 130 uM RNA in 10 mM MgCl2, 10 mM KCl, and 10 mM HEPES-KOH, pH 7.5; Reagent: 32% MPD, 40 mM SrCl2, 12 mM spermine, 40 mM sodium acetate, pH 4.6, and 0.8 mM iridium (III) ...Details: RNA solution: 130 uM RNA in 10 mM MgCl2, 10 mM KCl, and 10 mM HEPES-KOH, pH 7.5; Reagent: 32% MPD, 40 mM SrCl2, 12 mM spermine, 40 mM sodium acetate, pH 4.6, and 0.8 mM iridium (III) hexamine; RNA solution and reagent mixed 1:1

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.210.999946, 1.10532, 1.10482
SYNCHROTRONAPS 19-BM21.10062
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMay 25, 2016
ADSC QUANTUM 210r2CCDMar 17, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray2Double crystal, Si(111)
Radiation wavelength
IDWavelength (Å)Relative weight
10.9999461
21.105321
31.104821
41.100621
ReflectionResolution: 2.7→40 Å / Num. obs: 15638 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 15.2
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.712 / % possible all: 100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
SCALEPACKdata scaling
PHENIXphasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.71→40 Å / SU B: 14.244 / SU ML: 0.272 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.091 / ESU R Free: 0.302 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.226 434 4.9 %RANDOM
Rwork0.2 ---
obs0.202 8451 99.1 %-
Displacement parametersBiso mean: 83.61 Å2
Baniso -1Baniso -2Baniso -3
1-4.35 Å20 Å20 Å2
2--4.35 Å20 Å2
3----8.7 Å2
Refinement stepCycle: LAST / Resolution: 2.71→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1917 62 6 1985

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