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- PDB-6zxz: Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification -

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Basic information

Entry
Database: PDB / ID: 6zxz
TitleSarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification
ComponentsSarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification
KeywordsRNA / Ribosome / modification
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsEnnifar, E.
Funding support Austria, 3items
OrganizationGrant numberCountry
Austrian Science FundP27947 Austria
Austrian Science FundP31691 Austria
Austrian Research Promotion AgencyWest Austrian BioNMR 858017 Austria
Citation
Journal: Chem Sci / Year: 2020
Title: 2'- O -Trifluoromethylated RNA - a powerful modification for RNA chemistry and NMR spectroscopy.
Authors: Himmelstoss, M. / Erharter, K. / Renard, E. / Ennifar, E. / Kreutz, C. / Micura, R.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.
History
DepositionJul 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification
B: Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification
C: Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,71911
Polymers25,4703
Non-polymers2488
Water91951
1
A: Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5914
Polymers8,4901
Non-polymers1013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5523
Polymers8,4901
Non-polymers622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5754
Polymers8,4901
Non-polymers853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.412, 75.267, 52.981
Angle α, β, γ (deg.)90.000, 105.604, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: RNA chain Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification


Mass: 8490.089 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: RNA 1 volume Buffer (NaCl 80 mM, KCl 12 mM, MgCl2 20 mM, NaCaco pH7.0 40 mM, MPD 35 %, spermine tetrahydrochloride 12 mM) 1 volume

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 17179 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 40.53 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.23
Reflection shellResolution: 2.44→2.59 Å / Num. unique obs: 2748 / CC1/2: 0.359

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDS31 Jan 2020data reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DVZ

3dvz


Resolution: 2.44→46.97 Å / SU ML: 0.3907 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.3476
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.232 858 5 %
Rwork0.2106 16288 -
obs0.212 17146 99.47 %
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.32 Å2
Refinement stepCycle: LAST / Resolution: 2.44→46.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1698 8 51 1757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00181899
X-RAY DIFFRACTIONf_angle_d0.53082961
X-RAY DIFFRACTIONf_chiral_restr0.0242387
X-RAY DIFFRACTIONf_plane_restr0.003478
X-RAY DIFFRACTIONf_dihedral_angle_d12.2058906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.590.36571420.35852711X-RAY DIFFRACTION98.75
2.59-2.790.35881420.32112682X-RAY DIFFRACTION99.79
2.79-3.080.31811420.26632739X-RAY DIFFRACTION99.97
3.08-3.520.22261460.21112717X-RAY DIFFRACTION99
3.52-4.430.20551430.16442727X-RAY DIFFRACTION99.55
4.44-46.970.16331430.15922712X-RAY DIFFRACTION99.76

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