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- PDB-2f4u: Asite RNA + designer antibiotic -

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Basic information

Entry
Database: PDB / ID: 2f4u
TitleAsite RNA + designer antibiotic
Components5'-R(*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'
KeywordsRNA / Asite RNA / designer antibiotic
Function / homologyChem-AB6 / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMurray, J.B. / Meroueh, S.O. / Russell, R.J. / Lentzen, G. / Haddad, J. / Mobashery, S.
CitationJournal: Chem.Biol. / Year: 2006
Title: Interactions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site
Authors: Murray, J.B. / Meroueh, S.O. / Russell, R.J. / Lentzen, G. / Haddad, J. / Mobashery, S.
History
DepositionNov 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: 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

Downloads & links

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Assembly

Deposited unit
A: 5'-R(*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(*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)14,0113
Polymers13,4862
Non-polymers5251
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.100, 46.460, 89.500
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(*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: A-site RNA
#2: Chemical ChemComp-AB6 / (2R)-4-AMINO-N-((1R,2S,3R,4R,5S)-5-AMINO-4-[(2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-{2-[(3-AMINOPROPYL)AMINO]ETHOXY}-3-HYDROXYCYCLOHEXYL)-2-HYDROXYBUTANAMIDE


Mass: 524.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H44N6O9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.55 Å3/Da / Density % sol: 51.79 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorDate: Jun 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→23.23 Å / Num. all: 4451 / Num. obs: 4451 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.092 / Net I/σ(I): 5.8 / Scaling rejects: 300
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique all% possible all
2.6-2.690.4231.62799.8
2.69-2.83099.8
2.8-2.931899.5
2.93-3.082498.3
3.08-3.282697.3
3.28-3.532796.5
3.53-3.883698.7
3.88-4.443498.5
4.44-5.584295.8
5.58-23.234993.2

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Processing

Software
NameVersionClassificationNB
d*TREK7.1SSIdata processing
CNSrefinement
PDB_EXTRACT1.701data extraction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→23.23 Å / σ(F): 161 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.299 445 9.7 %Random
Rwork0.25 ---
all0.25 4451 --
obs0.299 4290 93.8 %-
Solvent computationBsol: 95.919 Å2
Displacement parametersBiso mean: 56.636 Å2
Baniso -1Baniso -2Baniso -3
1-7.806 Å20 Å20 Å2
2--11.806 Å20 Å2
3----19.611 Å2
Refinement stepCycle: LAST / Resolution: 2.6→23.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 892 36 32 960
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2dna-rna-multi-endo.param
X-RAY DIFFRACTION3893.par
X-RAY DIFFRACTION4CNS_TOPPAR:water.param

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