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- PDB-4ena: Crystal structure of fluoride riboswitch, soaked in Cs+ -

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Basic information

Entry
Database: PDB / ID: 4ena
TitleCrystal structure of fluoride riboswitch, soaked in Cs+
ComponentsFluoride riboswitch
KeywordsRNA / pseudoknot
Function / homology: / FLUORIDE ION / RNA / RNA (> 10)
Function and homology information
Biological speciesThermotoga petrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsRen, A.M. / Rajashankar, K.R. / Patel, D.J.
CitationJournal: Nature / Year: 2012
Title: Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch.
Authors: Ren, A. / Rajashankar, K.R. / Patel, D.J.
History
DepositionApr 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Feb 13, 2013Group: Structure summary
Revision 1.3Sep 13, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_leaving_atom_flag / _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_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: Fluoride riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,79114
Polymers16,9371
Non-polymers85413
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.742, 77.149, 42.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: RNA chain Fluoride riboswitch /


Mass: 16936.996 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription with T7 RNA polymerase.
Source: (synth.) Thermotoga petrophila (bacteria)
#2: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cs
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-F / FLUORIDE ION / Fluoride


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.1 M sodium cacodylate, pH 7.0, 20 mM spermine, 100 mM cesium chloride, 50 mM magnesium chloride, 20% MPD, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.85→20 Å / Num. obs: 4798 / Redundancy: 4.4 % / Rmerge(I) obs: 0.106 / Rsym value: 0.102 / Net I/σ(I): 13.7

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Processing

Software
NameVersionClassification
ADSCdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ENB

4enb


Resolution: 2.85→19.973 Å / SU ML: 0.52 / σ(F): 1.35 / Phase error: 27.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 459 10.19 %
Rwork0.2251 --
obs0.2292 4798 96.82 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.015 Å2 / ksol: 0.287 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.5137 Å2-0 Å20 Å2
2---17.1585 Å2-0 Å2
3---11.6449 Å2
Refinement stepCycle: LAST / Resolution: 2.85→19.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1122 13 19 1154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0361288
X-RAY DIFFRACTIONf_angle_d1.1262000
X-RAY DIFFRACTIONf_dihedral_angle_d16.86623
X-RAY DIFFRACTIONf_chiral_restr0.061259
X-RAY DIFFRACTIONf_plane_restr0.00952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.02810.42561380.43051265X-RAY DIFFRACTION96
3.0281-3.26090.31081370.27741258X-RAY DIFFRACTION96
3.2609-3.58740.30431420.24461235X-RAY DIFFRACTION96
3.5874-4.10260.25831450.20411264X-RAY DIFFRACTION97
4.1026-5.15410.23321420.1951285X-RAY DIFFRACTION98
5.1541-19.97360.22981530.19531246X-RAY DIFFRACTION97

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