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- PDB-3ivn: Structure of the U65C mutant A-riboswitch aptamer from the Bacill... -

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Basic information

Entry
Database: PDB / ID: 3ivn
TitleStructure of the U65C mutant A-riboswitch aptamer from the Bacillus subtilis pbuE operon
ComponentsA-riboswitch
KeywordsRNA / Aptamer / A-Riboswitch
Function / homologyBROMIDE ION / RNA / RNA (> 10)
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDelfosse, V. / Dagenais, P. / Chausse, D. / Di Tomasso, G. / Legault, P.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Riboswitch structure: an internal residue mimicking the purine ligand.
Authors: Delfosse, V. / Bouchard, P. / Bonneau, E. / Dagenais, P. / Lemay, J.F. / Lafontaine, D.A. / Legault, P.
History
DepositionSep 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: A-riboswitch
B: A-riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,52713
Polymers45,1492
Non-polymers37911
Water1,58588
1
A: A-riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8568
Polymers22,5741
Non-polymers2817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: A-riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6725
Polymers22,5741
Non-polymers974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.930, 46.330, 87.240
Angle α, β, γ (deg.)90.00, 120.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain A-riboswitch


Mass: 22574.332 Da / Num. of mol.: 2 / Mutation: U65C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Description: In vitro translation / Plasmid: ptZ19R-derived pTR-4 vector / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2 mM Spermine, 50 mM Na Cacodylate, 32% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.91924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91924 Å / Relative weight: 1
ReflectionResolution: 2.8→26.04 Å / Num. obs: 10839 / % possible obs: 99.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 31.7 Å2 / Rsym value: 0.13 / Net I/σ(I): 10.5
Reflection shellResolution: 2.8→2.93 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.63 / % possible all: 99

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.4_125)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB id 1Y26

1y26


Resolution: 2.8→26.039 Å / Occupancy max: 1 / Occupancy min: 0.51 / SU ML: 0.39 / σ(F): 2 / Phase error: 29.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.277 1083 9.99 %
Rwork0.227 9756 -
obs0.232 10839 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 11.234 Å2 / ksol: 0.276 e/Å3
Displacement parametersBiso max: 64.44 Å2 / Biso mean: 30.376 Å2 / Biso min: 14.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.052 Å20 Å28.326 Å2
2---10.795 Å20 Å2
3---10.847 Å2
Refinement stepCycle: LAST / Resolution: 2.8→26.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2932 11 88 3031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033278
X-RAY DIFFRACTIONf_angle_d1.1475104
X-RAY DIFFRACTIONf_dihedral_angle_d16.3211648
X-RAY DIFFRACTIONf_chiral_restr0.052688
X-RAY DIFFRACTIONf_plane_restr0.002138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8004-2.92770.42541350.33881219X-RAY DIFFRACTION99
2.9277-3.08180.32341340.29411202X-RAY DIFFRACTION100
3.0818-3.27450.31671310.24641198X-RAY DIFFRACTION100
3.2745-3.52680.25191360.22071220X-RAY DIFFRACTION100
3.5268-3.88070.27391350.20641217X-RAY DIFFRACTION99
3.8807-4.43980.25991350.19241214X-RAY DIFFRACTION100
4.4398-5.58460.23161360.19551217X-RAY DIFFRACTION99
5.5846-26.03980.22161410.19881269X-RAY DIFFRACTION99

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