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- PDB-4l81: Structure of the SAM-I/IV riboswitch (env87(deltaU92, deltaG93)) -

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Basic information

Entry
Database: PDB / ID: 4l81
TitleStructure of the SAM-I/IV riboswitch (env87(deltaU92, deltaG93))
ComponentsSAM-I/IV variant riboswitch aptamer domain
KeywordsRNA / Riboswitch / Gene regulation / SAM binding
Function / homologyCOBALT HEXAMMINE(III) / S-ADENOSYLMETHIONINE / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsTrausch, J.J. / Reyes, F.E. / Edwards, A.L. / Batey, R.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for diversity in the SAM clan of riboswitches.
Authors: Trausch, J.J. / Xu, Z. / Edwards, A.L. / Reyes, F.E. / Ross, P.E. / Knight, R. / Batey, R.T.
History
DepositionJun 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAM-I/IV variant riboswitch aptamer domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,24817
Polymers31,2541
Non-polymers1,99416
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.930, 120.930, 186.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: RNA chain SAM-I/IV variant riboswitch aptamer domain


Mass: 31253.779 Da / Num. of mol.: 1 / Fragment: aptamer domain / Source method: obtained synthetically / Details: in vitro T7 RNA polymerase transcript
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CoH18N6
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg

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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

Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM Na-cacodylate, pH 8.0, 40 mM magnesium acetate, 300 mM KCl, 7% 2-methyl-2,4-pentanediol (MPD), 1 mM cobalt hexammine, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2011
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→30 Å / Num. all: 32036 / Num. obs: 31972 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 7.52 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GIS

2gis


Resolution: 2.95→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.232 3095 RANDOM
Rwork0.219 --
obs0.219 31286 -
all-32113 -
Refine analyzeLuzzati coordinate error obs: 0.41 Å / Luzzati sigma a obs: 0.63 Å
Refinement stepCycle: LAST / Resolution: 2.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2075 96 0 2171
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00709
X-RAY DIFFRACTIONc_angle_deg1.19
X-RAY DIFFRACTIONc_dihedral_angle_d14.7
X-RAY DIFFRACTIONc_improper_angle_d1.722

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