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- PDB-3s4p: Crystal structure of the bacterial ribosomal decoding site comple... -

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Basic information

Entry
Database: PDB / ID: 3s4p
TitleCrystal structure of the bacterial ribosomal decoding site complexed with an amphiphilic paromomycin O2''-ether analogue
ComponentsRNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3')
KeywordsRNA/ANTIBIOTIC / aminoglycoside / antibiotics / ribosome / decoding site / RNA / RNA-ANTIBIOTIC complex
Function / homologyChem-JS6 / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.56 Å
AuthorsSzychowski, J. / Kondo, J. / Zahr, O. / Auclair, K. / Westhof, E. / Hanessian, S. / Keillor, J.W.
CitationJournal: Chemmedchem / Year: 2011
Title: Inhibition of aminoglycoside-deactivating enzymes APH(3')-IIIa and AAC(6')-Ii by amphiphilic paromomycin O2''-ether analogues
Authors: Szychowski, J. / Kondo, J. / Zahr, O. / Auclair, K. / Westhof, E. / Hanessian, S. / Keillor, J.W.
History
DepositionMay 20, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 1, 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_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(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3')
B: RNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0124
Polymers13,4862
Non-polymers1,5262
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-17 kcal/mol
Surface area8160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.189, 44.689, 94.585
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 6743.077 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized
#2: Chemical ChemComp-JS6 / (1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-2-O-{2-[(2-phenylethyl)amino]ethyl}-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside


Mass: 762.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H58N6O14
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sodium Cacodylate, Spermine, KCl, MPD, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.56→40.4 Å / Num. obs: 5003 / % possible obs: 99.6 %

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
AMoREphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J7T

1j7t


Resolution: 2.56→10 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8273 / σ(F): 65
RfactorNum. reflection% reflection
Rfree0.2671 501 10.2 %
Rwork0.2379 --
obs-4848 98.6 %
Solvent computationBsol: 36.3817 Å2
Displacement parametersBiso max: 92.19 Å2 / Biso mean: 47.9676 Å2 / Biso min: 14.54 Å2
Baniso -1Baniso -2Baniso -3
1--6.35 Å20 Å20 Å2
2--6.96 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.56→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 900 106 38 1044
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg0.895
X-RAY DIFFRACTIONc_mcbond_it0
X-RAY DIFFRACTIONc_scbond_it1.7312
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scangle_it2.6352.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.56-2.650.6031500.5405455
2.65-2.750.4429390.4134414453
2.75-2.880.444500.3903430480
2.88-3.020.3423430.3127432475
3.02-3.210.2741490.2225436485
3.21-3.450.2477520.2429443495
3.45-3.780.3118560.2261433489
3.78-4.280.2496490.201442491
4.28-5.260.1982530.2017444497
5.26-100.1992600.1807468528
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2rna_jw.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5JS136.paramJS136.top

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