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- PDB-2esi: Complex between Kanamycin A and the 16S-Rrna A Site. -

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Basic information

Entry
Database: PDB / ID: 2esi
TitleComplex between Kanamycin A and the 16S-Rrna A Site.
Components5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'
KeywordsRNA / RNA-AMINOGLYCOSIDE INTERACTIONS / A SITE / UOU PAIRS / AA BULGES
Function / homologyKANAMYCIN A / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWesthof, E.
CitationJournal: Nucleic Acids Res. / Year: 2005
Title: Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding
Authors: Francois, B. / Russel, R.J.M. / Murray, J.B. / Aboul-ela, F. / Masquida, B. / Vicens, Q. / Westhof, E.
History
DepositionOct 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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

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Assembly

Deposited unit
A: 5'-R(*UP*UP*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(*UP*UP*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)16,1645
Polymers14,7112
Non-polymers1,4533
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.380, 32.730, 52.700
Angle α, β, γ (deg.)90.00, 107.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 7355.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence contains the bacterial A-Site
#2: Chemical ChemComp-KAN / KANAMYCIN A


Mass: 484.499 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H36N4O11 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: MPD, NACL, MGSO4, GLYCEROL, NA CACODYLATE, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2NACL11
3MGSO411
4GLYCEROL11
5NA CACODYLATE11
6H2O11
7MPD12
8NACL12
9MGSO412
10NA CACODYLATE12
11H2O12

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.936 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.936 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 4500 / Num. obs: 2454 / Observed criterion σ(F): 5 / Observed criterion σ(I): 5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30 Å / σ(F): 1
Stereochemistry target values: G. PARKINSON, J. VOJTECHOVSKY, L. CLOWNEY, A.T. BRUNGER, H.M. BERMAN, NEW PARAMETERS FOR THE REFINEMENT OF NUCLEIC ACIDCONTAINING STRUCTURES, ACTA CRYST. D, 52,57-64 (1996)
RfactorNum. reflection% reflectionSelection details
Rfree0.2656 233 -RANDOM
Rwork0.2015 ---
all-3223 --
obs-2454 76.1 %-
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 932 99 34 1065
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_d1.1613
X-RAY DIFFRACTIONc_dihedral_angle_d11.257
X-RAY DIFFRACTIONc_improper_angle_d1.472

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