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- PDB-4nmg: 2'-Trifluoromethylthio-2'-deoxyuridine-modified SRL -

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Basic information

Entry
Database: PDB / ID: 4nmg
Title2'-Trifluoromethylthio-2'-deoxyuridine-modified SRL
Components23S ribosomal RNA Sarcin Ricin Loop
KeywordsRNA / RNA hairpin / structural
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.01 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 15, 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
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
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


Theoretical massNumber of molelcules
Total (without water)8,8301
Polymers8,8301
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.572, 29.572, 76.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 8830.335 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 1.89 Å3/Da / Density % sol: 35.08 %
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: 0.8 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: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.01→30 Å / Num. all: 68249 / Num. obs: 67951 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 18.73

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3DVZ

3dvz


Resolution: 1.01→29.572 Å / SU ML: 0.09 / σ(F): 1.48 / Phase error: 14.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.141 1713 5.02 %RANDOM
Rwork0.12 ---
obs0.121 67835 99.56 %-
all-68135 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.01→29.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 583 0 151 734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014716
X-RAY DIFFRACTIONf_angle_d1.8951124
X-RAY DIFFRACTIONf_dihedral_angle_d13.171354
X-RAY DIFFRACTIONf_chiral_restr0.086150
X-RAY DIFFRACTIONf_plane_restr0.03229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.01-1.0240.29331270.27022457X-RAY DIFFRACTION90
1.024-1.03930.23051420.2372676X-RAY DIFFRACTION100
1.0393-1.05550.27511410.22022694X-RAY DIFFRACTION100
1.0555-1.07290.23091440.20452686X-RAY DIFFRACTION100
1.0729-1.09140.2061420.19742748X-RAY DIFFRACTION100
1.0914-1.11120.21231440.1722679X-RAY DIFFRACTION100
1.1112-1.13260.17021390.152708X-RAY DIFFRACTION100
1.1326-1.15570.1611420.14182665X-RAY DIFFRACTION100
1.1557-1.18080.15291460.1322745X-RAY DIFFRACTION100
1.1808-1.20830.15491400.12952621X-RAY DIFFRACTION100
1.2083-1.23850.12181440.11612725X-RAY DIFFRACTION100
1.2385-1.2720.13251440.11552724X-RAY DIFFRACTION100
1.272-1.30940.14691420.11082652X-RAY DIFFRACTION100
1.3094-1.35170.14751440.1132721X-RAY DIFFRACTION100
1.3517-1.40.12421430.10342690X-RAY DIFFRACTION100
1.4-1.4560.16981390.10292661X-RAY DIFFRACTION100
1.456-1.52230.131410.10422687X-RAY DIFFRACTION100
1.5223-1.60260.13511420.09162723X-RAY DIFFRACTION100
1.6026-1.7030.10811430.08292687X-RAY DIFFRACTION100
1.703-1.83440.12391460.09032712X-RAY DIFFRACTION100
1.8344-2.0190.13381420.1042683X-RAY DIFFRACTION100
2.019-2.31110.12461420.11962699X-RAY DIFFRACTION100
2.3111-2.91130.15521420.13892702X-RAY DIFFRACTION100
2.9113-29.58470.11971420.10952687X-RAY DIFFRACTION100

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