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- PDB-3s7c: Crystal structure of a 2'-azido-uridine-modified RNA -

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Basic information

Entry
Database: PDB / ID: 3s7c
TitleCrystal structure of a 2'-azido-uridine-modified RNA
ComponentsEcoli 23 S rRNA Sarcin Ricin loop
KeywordsRNA / hairpin RNA / RNA labelling / 2'-azido-uridine
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.2Sep 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
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.610, 29.610, 76.180
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 35.4 %
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 NaEDTA, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. all: 26603 / Num. obs: 26490 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.1→1.13 Å / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 2.91 / % possible all: 94.3

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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: 1.1→29.61 Å / σ(F): 2.06 / Phase error: 20.9 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1559 1326 5.01 %
Rwork0.1166 --
obs0.118 26483 99.8 %
all-26477 -
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.04 Å2 / ksol: 0.435 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5863 Å20 Å2-0 Å2
2--0.5863 Å2-0 Å2
3----1.1725 Å2
Refine analyzeLuzzati coordinate error obs: 0.11 Å
Refinement stepCycle: LAST / Resolution: 1.1→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 581 0 198 779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005707
X-RAY DIFFRACTIONf_angle_d0.9691106
X-RAY DIFFRACTIONf_dihedral_angle_d17.137350
X-RAY DIFFRACTIONf_chiral_restr0.063146
X-RAY DIFFRACTIONf_plane_restr0.0129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1002-1.14420.24631440.21412733X-RAY DIFFRACTION93
1.1442-1.19630.22631470.20112787X-RAY DIFFRACTION95
1.1963-1.25940.1861470.17742798X-RAY DIFFRACTION95
1.2594-1.33830.18371480.16452805X-RAY DIFFRACTION95
1.3383-1.44160.17241470.16442805X-RAY DIFFRACTION95
1.4416-1.58670.16981460.15492771X-RAY DIFFRACTION95
1.5867-1.81620.13651480.12542813X-RAY DIFFRACTION95
1.8162-2.28810.15321490.11452819X-RAY DIFFRACTION95
2.2881-27.60720.13951490.06792826X-RAY DIFFRACTION95

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