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- PDB-4jf2: Structure of a class II preQ1 riboswitch reveals ligand recogniti... -

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Basic information

Entry
Database: PDB / ID: 4jf2
TitleStructure of a class II preQ1 riboswitch reveals ligand recognition by a new fold
ComponentsPreQ1-II Riboswitch
KeywordsRNA / Riboswitch / H-type Pseudoknot
Function / homology: / 7-DEAZA-7-AMINOMETHYL-GUANINE / RNA / RNA (> 10)
Function and homology information
Biological speciesLactobacillus rhamnosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.28 Å
AuthorsLiberman, J.A. / Wedekind, J.E.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold.
Authors: Liberman, J.A. / Salim, M. / Krucinska, J. / Wedekind, J.E.
History
DepositionFeb 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Jun 12, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 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 / pdbx_struct_special_symmetry / 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: PreQ1-II Riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,12121
Polymers24,8511
Non-polymers2,27020
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.036, 85.972, 98.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-35-

U

21A-76-

G

31A-261-

HOH

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Components

#1: RNA chain PreQ1-II Riboswitch


Mass: 24850.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: In vitro transcription / Source: (synth.) Lactobacillus rhamnosus (bacteria)
#2: Chemical ChemComp-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE


Mass: 179.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5O
#3: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cs
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 14.8% PEG 6000, 160 mM MgCl2, 50 mM Na-cacodylate pH 6.0, 1 mM spermine, 150 mM CsCl, Vapor Diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127 Å
DetectorType: Q315R / Detector: CCD / Date: Mar 18, 2012 / Details: Rh coated flat mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 12133 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.054 / Χ2: 1.01 / Net I/σ(I): 22.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.283.10.2818491.072167.2
2.28-2.373.80.28210981.008186
2.37-2.484.40.20412440.998199.8
2.48-2.614.40.14512660.997199.8
2.61-2.774.30.10812621.03199.2
2.77-2.994.40.06812551.003199.9
2.99-3.294.40.04312821.029199.5
3.29-3.764.20.04512670.985198.9
3.76-4.744.20.0412970.984199.1
4.74-503.90.03913131.027195.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1290refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.28→25.695 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.7879 / SU ML: 0.32 / σ(F): 1.34 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 1117 9.93 %Random
Rwork0.1925 ---
obs0.1977 11247 97.61 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.81 Å2 / Biso mean: 30.586 Å2 / Biso min: 5.17 Å2
Refine analyzeLuzzati coordinate error free: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.28→25.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1644 32 152 1828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081880
X-RAY DIFFRACTIONf_angle_d1.3682935
X-RAY DIFFRACTIONf_chiral_restr0.053384
X-RAY DIFFRACTIONf_plane_restr0.00878
X-RAY DIFFRACTIONf_dihedral_angle_d14.62925
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2801-2.38380.3251190.23191132125188
2.3838-2.50940.32191410.234112601401100
2.5094-2.66650.36981400.24412791419100
2.6665-2.87210.2931410.24241277141899
2.8721-3.16070.28041420.192312731415100
3.1607-3.6170.20061440.16161282142699
3.617-4.55290.18411420.15271291143399
4.5529-25.69710.23961480.2041336148497
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.5179-0.6191-1.2522-0.15910.22110.64910.20180.20890.1095-0.1130.0031-0.104-0.318-0.18890.1290.2255-0.00520.07540.368-0.0420.202412.213731.674729.142
22.8075-2.75481.80263.036-1.11732.13640.3067-1.55980.59461.23730.03010.8607-0.0533-0.54832.33350.4912-0.20930.24060.4698-0.28990.3358-6.473432.77864.084
33.33741.0941-0.91551.2589-0.73640.3059-0.06010.2208-0.3571-0.1682-0.0351-0.1818-0.0053-0.0415-0.12880.1841-0.00420.01340.1414-0.03850.17782.527621.233246.5271
46.1998-0.2817-0.19055.6097-0.0022.5072-0.4591-1.81020.33081.31950.01660.4016-0.33340.7271-1.82290.3061-0.16630.07120.02790.0482-0.1328-0.954723.707165.0851
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 29 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 35 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 69 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 77 )A0

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