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- PDB-4nlf: 2'-trifluoromethylthio-2'-deoxycytidine-modified SRL -

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Basic information

Entry
Database: PDB / ID: 4nlf
Title2'-trifluoromethylthio-2'-deoxycytidine-modified SRL
Components23S ribosomal RNA Sarcin Ricin Loop
KeywordsRNA / RNA Hairpin / structural
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsEnnifar, E. / Micura, R. / Kosutic, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Surprising base pairing and structural properties of 2'-trifluoromethylthio-modified ribonucleic acids.
Authors: Kosutic, M. / Jud, L. / Da Veiga, C. / Frener, M. / Fauster, K. / Kreutz, C. / Ennifar, E. / Micura, R.
History
DepositionNov 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 23S ribosomal RNA Sarcin Ricin Loop
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9262
Polymers8,8301
Non-polymers961
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.170, 39.570, 29.920
Angle α, β, γ (deg.)90.00, 90.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain 23S ribosomal RNA Sarcin Ricin Loop


Mass: 8830.334 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 1.96 Å3/Da / Density % sol: 37.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1:1 RNA (in 1.0 mM sodium EDTA, pH 8.0, 10 mM Tris, pH 8.0) to well solution (3.1 M ammonium sulfate, 50 mM potassium MOPS, 10 mM magnesium chloride, 10 mM manganese chloride), VAPOR ...Details: 1:1 RNA (in 1.0 mM sodium EDTA, pH 8.0, 10 mM Tris, pH 8.0) to well solution (3.1 M ammonium sulfate, 50 mM potassium MOPS, 10 mM magnesium chloride, 10 mM manganese chloride), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.708 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 28, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.708 Å / Relative weight: 1
ReflectionResolution: 1→30 Å / Num. all: 72332 / Num. obs: 69037 / % possible obs: 95.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 38.78
Reflection shellResolution: 1→1.03 Å / Redundancy: 5 % / Rmerge(I) obs: 0.093 / Mean I/σ(I) obs: 15.8 / Num. unique all: 5324 / % possible all: 91.2

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DVZ

3dvz


Resolution: 1→29.166 Å / SU ML: 0.03 / σ(F): 2.04 / Phase error: 8.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1163 1204 3.43 %RANDOM
Rwork0.0985 ---
obs0.0991 35121 95.36 %-
all-36830 --
Solvent computationShrinkage radii: 0.4 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1→29.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 583 5 183 771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008671
X-RAY DIFFRACTIONf_angle_d1.5231051
X-RAY DIFFRACTIONf_dihedral_angle_d13.763332
X-RAY DIFFRACTIONf_chiral_restr0.065138
X-RAY DIFFRACTIONf_plane_restr0.02828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.040.09351250.07993605X-RAY DIFFRACTION92
1.04-1.08740.09381380.07293642X-RAY DIFFRACTION93
1.0874-1.14470.09471260.07413709X-RAY DIFFRACTION94
1.1447-1.21640.08871390.07443711X-RAY DIFFRACTION95
1.2164-1.31040.08631310.07543770X-RAY DIFFRACTION95
1.3104-1.44220.10931350.08463788X-RAY DIFFRACTION96
1.4422-1.65090.10161340.08723836X-RAY DIFFRACTION97
1.6509-2.07990.11171350.10123876X-RAY DIFFRACTION98
2.0799-29.17860.15561410.1293980X-RAY DIFFRACTION99

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