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- PDB-5ns3: Crystal structures of Cy5 cyanine fluorophores stacked onto the e... -

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Basic information

Entry
Database: PDB / ID: 5ns3
TitleCrystal structures of Cy5 cyanine fluorophores stacked onto the end of double-stranded RNA
Components
  • 50S ribosomal protein L5
  • double-stranded RNA
KeywordsRNA / Cy5 / fluorophore
Function / homology
Function and homology information


tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex
Similarity search - Function
Ribosomal protein L5, bacterial-type / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Large ribosomal subunit protein uL5
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsLiu, Y.J. / Lilley, D.M.J.
CitationJournal: Biophys. J. / Year: 2017
Title: Crystal Structures of Cyanine Fluorophores Stacked onto the End of Double-Stranded RNA.
Authors: Liu, Y. / Lilley, D.M.J.
History
DepositionApr 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 50S ribosomal protein L5
B: 50S ribosomal protein L5
C: double-stranded RNA
D: double-stranded RNA


Theoretical massNumber of molelcules
Total (without water)62,9444
Polymers62,9444
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-42 kcal/mol
Surface area22950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.043, 123.895, 51.201
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 50S ribosomal protein L5 / TL4 / TthL5


Mass: 20475.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: rplE, rpl5 / Production host: Escherichia coli (E. coli) / References: UniProt: P41201
#2: RNA chain double-stranded RNA


Mass: 10995.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.3 M Magnesium formate dehydrate 0.1 M BIS-TRIS pH 5.5 50mM KF

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Data collection

DiffractionMean temperature: 94 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.987→47.52 Å / Num. all: 278257 / Num. obs: 42321 / % possible obs: 99 % / Redundancy: 6.6 % / Biso Wilson estimate: 49.61 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.07599 / Rrim(I) all: 0.08279 / Net I/σ(I): 15.77
Reflection shellResolution: 1.987→2.058 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.275 / Mean I/σ(I) obs: 1.44 / Num. unique all: 26351 / Num. unique obs: 4055 / CC1/2: 0.561 / Rrim(I) all: 1.386 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACT3.22data extraction
xia2data reduction
PHENIXphasing
RefinementResolution: 2.4→47.521 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2745 1227 5.05 %
Rwork0.2519 --
obs0.253 24293 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.57 Å2 / Biso mean: 35.2941 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.4→47.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2213 1370 0 14 3597
Biso mean---44.26 -
Num. residues----339

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