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- PDB-5ns4: Crystal structures of Cy3 cyanine fluorophores stacked onto the e... -

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Basic information

Entry
Database: PDB / ID: 5ns4
TitleCrystal structures of Cy3 cyanine fluorophores stacked onto the end of double-stranded RNA
Components
  • 50S ribosomal protein L5
  • RNA (34-MER)
KeywordsRNA BINDING PROTEIN / Cy3 / fluorophores / RNA
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
Chem-96T / RNA / RNA (> 10) / Large ribosomal subunit protein uL5
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLiu, Y.J. / Lilley, D.M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
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 1.1Jan 17, 2024Group: 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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: RNA (34-MER)
D: RNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,85212
Polymers62,2374
Non-polymers6168
Water1,29772
1
A: 50S ribosomal protein L5
C: RNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6858
Polymers31,1182
Non-polymers5676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-38 kcal/mol
Surface area13020 Å2
MethodPISA
2
B: 50S ribosomal protein L5
D: RNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1674
Polymers31,1182
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-30 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.757, 122.432, 51.013
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: 20590.947 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 RNA (34-MER)


Mass: 10527.345 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Thermus thermophilus (bacteria)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-96T / 3-[(2~{Z})-2-[(~{E})-3-[3,3-dimethyl-1-(3-oxidanylpropyl)indol-1-ium-2-yl]prop-2-enylidene]-3,3-dimethyl-indol-1-yl]propan-1-ol


Mass: 445.616 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C29H37N2O2 / Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Thermus thermophilus (bacteria)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 50 mM sodium cacodylate at pH 6.5, 100 mM Mg(CH3COO)2, 50 mM KF, 15% PEG 8000 drop

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979601 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979601 Å / Relative weight: 1
ReflectionResolution: 2.4→46.88 Å / Num. obs: 23654 / % possible obs: 100 % / Redundancy: 4.4 % / Biso Wilson estimate: 48.88 Å2 / Rmerge(I) obs: 0.09978 / Rrim(I) all: 0.1141 / Net I/σ(I): 12.48
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 6.26 / Num. unique obs: 2309 / Rrim(I) all: 0.1834 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimlessdata scaling
PDB_EXTRACT3.22data extraction
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MJI

1mji


Resolution: 2.4→46.88 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29
RfactorNum. reflection% reflection
Rfree0.283 1195 5.07 %
Rwork0.2598 --
obs0.261 23593 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.67 Å2 / Biso mean: 37.1008 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.4→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2297 1325 7 72 3701
Biso mean--30.11 41.44 -
Num. residues----346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133801
X-RAY DIFFRACTIONf_angle_d1.5315404
X-RAY DIFFRACTIONf_chiral_restr0.096664
X-RAY DIFFRACTIONf_plane_restr0.008464
X-RAY DIFFRACTIONf_dihedral_angle_d13.61648
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.49610.32511190.316124562575100
2.4961-2.60970.34541420.324124532595100
2.6097-2.74730.35871340.331124272561100
2.7473-2.91940.30411360.320224562592100
2.9194-3.14480.30231330.307424852618100
3.1448-3.46110.30021270.262624762603100
3.4611-3.96170.27311310.249424992630100
3.9617-4.99050.25751340.21982508264299
4.9905-47.09820.261390.23622638277799

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