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- PDB-4enb: Crystal structure of fluoride riboswitch, bound to Iridium -

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Basic information

Entry
Database: PDB / ID: 4enb
TitleCrystal structure of fluoride riboswitch, bound to Iridium
ComponentsFluoride riboswitch
KeywordsRNA / pseudoknot
Function / homologyFLUORIDE ION / IRIDIUM HEXAMMINE ION / : / RNA / RNA (> 10)
Function and homology information
Biological speciesThermotoga petrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.302 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 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Fluoride riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,34314
Polymers16,9371
Non-polymers1,40613
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.949, 76.466, 42.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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RNA chain , 1 types, 1 molecules A

#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)

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Non-polymers , 5 types, 48 molecules

#2: Chemical
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H18IrN6
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.1 M sodium cacodylate, pH 7.0, 20 mM spermine, 0.2 M strontium 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: 2.3→50 Å / Num. obs: 8596 / Redundancy: 4.5 % / Rmerge(I) obs: 0.058 / Rsym value: 0.122 / Net I/σ(I): 34.2

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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: SAD / Resolution: 2.302→46.185 Å / SU ML: 0.37 / σ(F): 1.39 / Phase error: 27.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2534 855 9.95 %
Rwork0.225 --
obs0.2279 8596 99.72 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.477 Å2 / ksol: 0.375 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.4906 Å2-0 Å2-0 Å2
2---9.1137 Å20 Å2
3---13.6043 Å2
Refinement stepCycle: LAST / Resolution: 2.302→46.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1122 13 35 1170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0291296
X-RAY DIFFRACTIONf_angle_d0.8312046
X-RAY DIFFRACTIONf_dihedral_angle_d13.859623
X-RAY DIFFRACTIONf_chiral_restr0.068259
X-RAY DIFFRACTIONf_plane_restr0.00852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.302-2.37020.39781310.34481205X-RAY DIFFRACTION98
2.3702-2.44670.38811360.32771198X-RAY DIFFRACTION100
2.4467-2.53420.34991300.31321234X-RAY DIFFRACTION100
2.5342-2.63560.33711360.33121233X-RAY DIFFRACTION100
2.6356-2.75550.3241290.32251216X-RAY DIFFRACTION100
2.7555-2.90080.33741390.31371223X-RAY DIFFRACTION100
2.9008-3.08250.32451370.26311227X-RAY DIFFRACTION100
3.0825-3.32050.29771390.25871207X-RAY DIFFRACTION100
3.3205-3.65450.22411370.241215X-RAY DIFFRACTION100
3.6545-4.1830.25121380.19461225X-RAY DIFFRACTION100
4.183-5.26890.19561320.15761219X-RAY DIFFRACTION100
5.2689-46.19410.18761330.17581225X-RAY DIFFRACTION100

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