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- PDB-1mwl: Crystal structure of geneticin bound to the eubacterial 16S rRNA ... -

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Basic information

Entry
Database: PDB / ID: 1mwl
TitleCrystal structure of geneticin bound to the eubacterial 16S rRNA A site
Components5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'
KeywordsRNA / AMINOGLYCOSIDE ANTIBIOTIC / GENETICIN-A-SITE COMPLEX / 16S RIBOSOMAL RNA / Bulged adenines / UoU pairs
Function / homologyGENETICIN / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsVicens, Q. / Westhof, E.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide
Authors: Vicens, Q. / Westhof, E.
#1: Journal: Chem.Biol. / Year: 2002
Title: Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding A site
Authors: Vicens, Q. / Westhof, E.
#2: Journal: Structure / Year: 2001
Title: Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site
Authors: Vicens, Q. / Westhof, E.
History
DepositionSep 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2012Group: Derived calculations
Revision 1.4Feb 14, 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 / 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: 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'
B: 5'-R(*CP*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)15,0904
Polymers14,0972
Non-polymers9932
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.200, 33.180, 51.740
Angle α, β, γ (deg.)90.00, 104.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 7048.259 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: eubacterial 16S rRNA A site. The oligonucleotide contains two A sites.
#2: Chemical ChemComp-GET / GENETICIN / G418


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


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: MPD, MAGNESIUM SULPHATE, POTASSIUM CHLORIDE, SODIUM CHLORIDE, SODIUM CACODYLATE, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Crystal grow
*PLUS
Temperature: 37 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.5-3.5 %MPD1drop
21.0-2.0 %(v/v)glycerol1drop
32 mMgeneticin1drop
4150 mM1dropKCl
550 mMsodium cacodylate1droppH6.4
640 %MPD1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.934
SYNCHROTRONESRF ID14-120.934
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDNov 7, 2001
ADSC QUANTUM 42CCDMar 11, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DIAMONDSINGLE WAVELENGTHMx-ray1
2GERMANIUM, DIAMONDSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 5466 / % possible obs: 88.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 65.5 Å2 / Rsym value: 0.062 / Net I/σ(I): 39.3
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 6.7 / Num. unique all: 566 / Rsym value: 0.211 / % possible all: 92.8
Reflection
*PLUS
Num. measured all: 24145 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
Highest resolution: 2.4 Å / % possible obs: 92.8 % / Num. unique obs: 566 / Rmerge(I) obs: 0.211

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LC4 (RNA ONLY)

1lc4


Resolution: 2.4→22.61 Å / Rfactor Rfree error: 0.014 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.5
Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, New parameters for the refinement of nucleic acid containing structures, Acta Cryst, D, 52, 57-64 (1996)
RfactorNum. reflection% reflectionSelection details
Rfree0.249 296 5.5 %RANDOM
Rwork0.224 ---
obs0.224 5334 86.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.9452 Å2 / ksol: 0.314673 e/Å3
Displacement parametersBiso mean: 57.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error free: 0.39 Å / Luzzati sigma a free: 0.45 Å
Refinement stepCycle: LAST / Resolution: 2.4→22.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 898 68 40 1006
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d10.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.119 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.556 22 4.4 %
Rwork0.386 479 -
obs--82.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1DNA-RNA_REP-MODIF.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3GENETICIN.PARAMGENETICIN.TOP
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg10.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
LS refinement shell
*PLUS
Highest resolution: 2.4 Å

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