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- PDB-2et8: Complex Between Neamine and the 16S-RRNA A-Site -

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Basic information

Entry
Database: PDB / ID: 2et8
TitleComplex Between Neamine and the 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 / RNA-AMINOGLYCOSIDE INTERACTIONS / A SITE / UOU PAIRS / AA BULGES
Function / homologyChem-XXX / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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. / Russell, R.J. / Murray, J.B. / Aboul-ela, F. / Masquida, B. / Vicens, Q. / Westhof, E.
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)14,4193
Polymers14,0972
Non-polymers3221
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.055, 47.310, 85.343
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: ESCHERICHIA COLI 16S RRNA A SITE
#2: Sugar ChemComp-XXX / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside / (2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYLOXY)-5-AMINO-2-(AMINOMETHYL)-TETRAHYDRO-2H-PYRA N-3,4-DIOL / NEOMYCIN A / NEAMINE / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucoside / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-D-glucoside / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-glucoside / Neamine


Type: D-saccharide / Mass: 322.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26N4O6 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
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
2NACLSodium chloride11
3MGSO411
4GLYCEROL11
5NA CACODYLATE11
6H2O11
7MPD12
8NACLSodium chloride12
9MGSO412
10NA CACODYLATE12

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.936 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.936 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 6000 / Num. obs: 6000 / 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
Starting model: PDB Entry: 1J7T

1j7t


Resolution: 2.5→50 Å / σ(F): 1
Stereochemistry target values: G. PARKINSON, J. VOJTECHOVSKY, L. CLOWNEY,A.T. BRUNGER, H.M. BERMAN, NEW PARAMETERSFOR THE REFINEMENT OF NUCLEIC ACID CONTAINING STRUCTURES, ACTA CRYST. D, 52,57-64 (1996)
RfactorNum. reflection% reflectionSelection details
Rfree0.2801 408 -RANDOM
Rwork0.265 ---
obs0.265 4239 85.1 %-
all-4982 --
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 898 22 21 941
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0059
X-RAY DIFFRACTIONc_angle_d1.155
X-RAY DIFFRACTIONc_dihedral_angle_d15.504
X-RAY DIFFRACTIONc_improper_angle_d1.4856

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