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- PDB-3s8u: Crystal structure of a 2-azido-adenine-modified RNA -

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Basic information

Entry
Database: PDB / ID: 3s8u
TitleCrystal structure of a 2-azido-adenine-modified RNA
ComponentsEcoli 23 S rRNA Sarcin Ricin loop
KeywordsRNA / hairpin RNA / RNA labelling / 2'-azido-adenine
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsEnnifar, E. / Micura, R.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: 2'-Azido RNA, a Versatile Tool for Chemical Biology: Synthesis, X-ray Structure, siRNA Applications, Click Labeling.
Authors: Fauster, K. / Hartl, M. / Santner, T. / Aigner, M. / Kreutz, C. / Bister, K. / Ennifar, E. / Micura, R.
History
DepositionMay 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ecoli 23 S rRNA Sarcin Ricin loop


Theoretical massNumber of molelcules
Total (without water)8,7701
Polymers8,7701
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.570, 29.570, 76.340
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 Ecoli 23 S rRNA Sarcin Ricin loop


Mass: 8770.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 1.9 Å3/Da / Density % sol: 35.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1 volume of [3.1M (NH4)2SO4, 50mM MOPS pH7.0, 10mM MgCl2, 10mM MnCl2] + 2 volumes of [RNA in 1mM EDTA, 10mM Tris pH8.0], VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2011
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. all: 20495 / Num. obs: 19989 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.114
Reflection shellResolution: 1.2→1.23 Å / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.67 / Num. unique all: 1549 / % possible all: 91.1

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DVZ

3dvz


Resolution: 1.2→27.574 Å / SU ML: 0.13 / σ(F): 2.01 / Phase error: 15.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1785 1000 5.01 %RANDOM
Rwork0.1428 ---
obs0.1445 19980 97.67 %-
all-20495 --
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.085 Å2 / ksol: 0.456 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6349 Å20 Å20 Å2
2--1.6349 Å20 Å2
3---0.4249 Å2
Refinement stepCycle: LAST / Resolution: 1.2→27.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 581 0 162 743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019707
X-RAY DIFFRACTIONf_angle_d1.7841106
X-RAY DIFFRACTIONf_dihedral_angle_d16.888348
X-RAY DIFFRACTIONf_chiral_restr0.1148
X-RAY DIFFRACTIONf_plane_restr0.03329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2001-1.26340.21711370.19082593X-RAY DIFFRACTION94
1.2634-1.34250.20971450.15562752X-RAY DIFFRACTION99
1.3425-1.44620.18611430.14292723X-RAY DIFFRACTION99
1.4462-1.59170.19981430.1252722X-RAY DIFFRACTION99
1.5917-1.8220.16381450.11452751X-RAY DIFFRACTION99
1.822-2.29540.16951440.1342722X-RAY DIFFRACTION98
2.2954-27.5810.17251430.1532717X-RAY DIFFRACTION97

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