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- PDB-4p20: Crystal structures of the bacterial ribosomal decoding site compl... -

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Basic information

Entry
Database: PDB / ID: 4p20
TitleCrystal structures of the bacterial ribosomal decoding site complexed with amikacin
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/ANTIBIOTIC / AMINOGLYCOSIDE / HABA GROUP / RIBOSOMAL DECODING SITE / X-RAY ANALYSIS / RNA / AMIKACIN / RNA-ANTIBIOTIC complex
Function / homologyChem-AKN / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsKondo, J. / Francois, B. / Russell, R.J.M. / Murray, J.B. / Westhof, E.
CitationJournal: Biochimie / Year: 2006
Title: Crystal structure of the bacterial ribosomal decoding site complexed with amikacin containing the gamma-amino-alpha-hydroxybutyryl (haba) group.
Authors: Kondo, J. / Francois, B. / Russell, R.J. / Murray, J.B. / Westhof, E.
History
DepositionFeb 28, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionMay 7, 2014ID: 2G5Q
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / pdbx_database_status ...citation / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _pdbx_database_status.pdb_format_compatible ..._citation.journal_id_CSD / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / refine_hist
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)15,8824
Polymers14,7112
Non-polymers1,1712
Water1,35175
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-23 kcal/mol
Surface area7660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.550, 32.820, 52.660
Angle α, β, γ (deg.)90.000, 108.710, 90.000
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 / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-AKN / (2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S ,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide / AMIKACIN


Mass: 585.603 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H43N5O13 / Comment: medication, antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 53.51 %
Crystal growTemperature: 310 K / Method: vapor diffusion / pH: 6.4 / Details: MPF, Na Cacodylate, NaCl, KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9357 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9357 Å / Relative weight: 1
ReflectionResolution: 2.7→32.82 Å / Num. obs: 4398 / % possible obs: 100 % / Redundancy: 3.59 % / Rmerge(I) obs: 0.16 / Χ2: 0.96 / Net I/σ(I): 4.8 / Num. measured all: 15897 / Scaling rejects: 120
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
2.7-2.83.610.432216074450.590100
2.8-2.913.670.3042.615554240.610100
2.91-3.043.660.2692.815784310.650100
3.04-3.23.660.1674.415964340.927100
3.2-3.43.660.1515.216084360.991399.8
3.4-3.663.630.1485.416464471.012299.8
3.66-4.033.610.137.215584261.172099.8
4.03-4.613.620.185.215994391.248100
4.61-5.813.520.1595.915954501.1711100
5.81-32.823.250.1327.915554661.3239100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→10 Å / FOM work R set: 0.807 / Cross valid method: FREE R-VALUE / σ(F): 179
RfactorNum. reflection% reflection
Rfree0.2679 425 9.9 %
Rwork0.2134 3693 -
obs-4118 95.7 %
Solvent computationBsol: 64.5977 Å2
Displacement parametersBiso max: 120.73 Å2 / Biso mean: 45.5528 Å2 / Biso min: 10.2 Å2
Baniso -1Baniso -2Baniso -3
1--9.8 Å20 Å211.57 Å2
2--1.774 Å20 Å2
3---8.026 Å2
Refinement stepCycle: final / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 898 80 75 1053
Biso mean--42.97 39.55 -
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_scbond_it5.0082
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scangle_it6.9692.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5amika_xplor.param

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