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- PDB-4k32: Crystal structure of geneticin bound to the leishmanial rRNA A-site -

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Basic information

Entry
Database: PDB / ID: 4k32
TitleCrystal structure of geneticin bound to the leishmanial rRNA A-site
ComponentsRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*UP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')
KeywordsRNA/antibiotic / rRNA duplex / Ribosomal A-site / Aminoglycoside / Leishmanial ribosome / RNA / RNA-antibiotic complex
Function / homologyGENETICIN / RNA / RNA (> 10)
Function and homology information
Biological speciesLeishmania (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShalev, M. / Kondo, J. / Adir, N. / Baasov, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Identification of the molecular attributes required for aminoglycoside activity against Leishmania.
Authors: Shalev, M. / Kondo, J. / Kopelyanskiy, D. / Jaffe, C.L. / Adir, N. / Baasov, T.
History
DepositionApr 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*UP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')
B: RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*UP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7064
Polymers14,7132
Non-polymers9932
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-49 kcal/mol
Surface area8280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.080, 90.760, 47.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: RNA chain RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*UP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')


Mass: 7356.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Leishmania (eukaryote)
#2: Chemical ChemComp-GET / GENETICIN / G418 / G418


Mass: 496.552 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H40N4O10 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM Na cacodylate, 1 mM spermine tetrahydrochloride, 1-20% 2-methyl-2,4-pentadiol (vs. 40% reservoir), 100-200 mM KCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9394 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9394 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 21134 / Num. obs: 4294 / % possible obs: 81.6 % / Observed criterion σ(F): 21.5 / Observed criterion σ(I): 21.5 / Rmerge(I) obs: 0.046
Reflection shellResolution: 2.5→2.57 Å / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2 / % possible all: 84.7

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→23.505 Å / SU ML: 0.41 / σ(F): 2.04 / Phase error: 25.06 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2445 429 10 %
Rwork0.2058 --
obs0.2096 4290 81.64 %
all-4290 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.954 Å2 / ksol: 0.403 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5826 Å2-0 Å20 Å2
2---7.1484 Å20 Å2
3---5.5658 Å2
Refinement stepCycle: LAST / Resolution: 2.5→23.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 898 68 11 977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061137
X-RAY DIFFRACTIONf_angle_d0.9541766
X-RAY DIFFRACTIONf_dihedral_angle_d16.821581
X-RAY DIFFRACTIONf_chiral_restr0.057254
X-RAY DIFFRACTIONf_plane_restr0.00845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5004-2.86160.34861430.31861295X-RAY DIFFRACTION85
2.8616-3.60330.29871440.21021300X-RAY DIFFRACTION83
3.6033-23.5060.19561420.17681266X-RAY DIFFRACTION77

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