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- PDB-4k31: Crystal structure of apramycin bound to the leishmanial rRNA A-site -

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Basic information

Entry
Database: PDB / ID: 4k31
TitleCrystal structure of apramycin 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 / Ribosome / RNA / RNA-antibiotic complex
Function / homologyAPRAMYCIN / RNA / RNA (> 10)
Function and homology information
Biological speciesLeishmania (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.415 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 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
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')
C: 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)16,8716
Polymers14,7132
Non-polymers2,1584
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-63 kcal/mol
Surface area8260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.790, 32.790, 107.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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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-AM2 / APRAMYCIN / NEBRAMYCIN II / 4-O-(3ALPHA-AMINO-6ALPHA-((4-AMINO-4-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY)-2,3,4,5ABETA,6,7,8,8AALPHA-OCTAHYDRO-8BETA-HYDROXY-7BETA-(METHYLAMINO)PYRANO(3,2-B)PYRAN-2ALPHA-YL)-2-DEOXY-D-STREPTAMINE


Mass: 539.577 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H41N5O11 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM Na cacodylate, 1 mM spermine tetrahydrochloride, 1% 2-methyl-2,4-pentadiol (vs. 40% reservoir), 100-250 mM NaCl, 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 / Date: Jan 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9394 Å / Relative weight: 1
ReflectionResolution: 1.4→35.8 Å / Num. all: 67545 / Num. obs: 23325 / % possible obs: 94.5 % / Observed criterion σ(F): 21.5 / Observed criterion σ(I): 21.5 / Redundancy: 2.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 14.1
Reflection shellResolution: 1.42→1.49 Å / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 5.7 / % possible all: 98

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.1_357) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2G5K

2g5k


Resolution: 1.415→19.51 Å / SU ML: 0.19 / σ(F): 2 / Phase error: 21.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2644 1190 5.11 %RANDOM
Rwork0.2258 ---
obs0.2277 23271 94.51 %-
all-22089 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.6 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.415→19.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 938 148 209 1295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061208
X-RAY DIFFRACTIONf_angle_d0.9761872
X-RAY DIFFRACTIONf_dihedral_angle_d15.785638
X-RAY DIFFRACTIONf_chiral_restr0.051288
X-RAY DIFFRACTIONf_plane_restr0.00944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4151-1.47950.28271650.24562826X-RAY DIFFRACTION98
1.4795-1.55740.23231670.22222929X-RAY DIFFRACTION100
1.5574-1.65490.24021440.21652921X-RAY DIFFRACTION100
1.6549-1.78260.22341570.20772908X-RAY DIFFRACTION100
1.7826-1.96190.22911370.21142941X-RAY DIFFRACTION100
1.9619-2.24540.22391670.20522904X-RAY DIFFRACTION100
2.2454-2.82760.28461590.22192912X-RAY DIFFRACTION99
2.8276-19.51160.3155940.25661740X-RAY DIFFRACTION60

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