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- PDB-1byj: GENTAMICIN C1A A-SITE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1byj
TitleGENTAMICIN C1A A-SITE COMPLEX
ComponentsRNA (16S RNA)
KeywordsRNA / COMPLEX (AMINOGLYCOSIDE-RIBOSOMAL RNA)
Function / homologyChem-GE1 / 3,5-DIAMINO-CYCLOHEXANOL / Chem-GE3 / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsYoshizawa, S. / Fourmy, D. / Puglisi, J.D.
CitationJournal: EMBO J. / Year: 1998
Title: Structural origins of gentamicin antibiotic action.
Authors: Yoshizawa, S. / Fourmy, D. / Puglisi, J.D.
History
DepositionOct 16, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / 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.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (16S RNA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1104
Polymers8,6561
Non-polymers4543
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)38 / 38LEAST RESTRAINT VIOLATION
RepresentativeModel #2

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Components

#1: RNA chain RNA (16S RNA)


Mass: 8656.185 Da / Num. of mol.: 1 / Fragment: DECODING REGION / Source method: obtained synthetically / Details: 16S RNA WAS CHEMICALLY SYNTHESIZED.
#2: Sugar ChemComp-GE1 / 2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranose / 3,4-DIDEOXY-2,6-AMINO-ALPHA-D GALACTOPYRANOSE / 2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexose / 2,6-diamino-2,3,4,6-tetradeoxy-D-erythro-hexose / 2,6-diamino-2,3,4,6-tetradeoxy-erythro-hexose


Type: D-saccharide, alpha linking / Mass: 146.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14N2O2
#3: Chemical ChemComp-GE2 / 3,5-DIAMINO-CYCLOHEXANOL


Mass: 130.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N2O
#4: Sugar ChemComp-GE3 / 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranose / 5-METHYL-4-METHYLAMINO-TETRAHYDRO-PYRAN-2,3,5-TRIOL / 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinose / 3-deoxy-4-C-methyl-3-(methylamino)-L-arabinose / 3-deoxy-4-C-methyl-3-(methylamino)-arabinose


Type: L-saccharide, beta linking / Mass: 177.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D
1213D
1314D-NOESY
141COSY
151TOCSY
NMR detailsText: A TOTAL OF 326 RNA, 7 GENTAMICIN AND 46 GENTAMICIN-RNA RESTRAINTS WERE USED. 111 EXPERIMENTAL DIHEDRAL RESTRAINTS WERE USED. FOR 38 THE FINAL STRUCTURES DEVIATIONS FROM EXPERIMENTAL RESTRAINTS ...Text: A TOTAL OF 326 RNA, 7 GENTAMICIN AND 46 GENTAMICIN-RNA RESTRAINTS WERE USED. 111 EXPERIMENTAL DIHEDRAL RESTRAINTS WERE USED. FOR 38 THE FINAL STRUCTURES DEVIATIONS FROM EXPERIMENTAL RESTRAINTS ARE: RMSD NMR DISTANCE RESTRAINTS (379) (A): 0.0249 (0.0002) RMSD NMR DIHEDRAL RESTRAINTS (111) (DEG): 0.0127 (0.0016) DEVIATIONS FROM DEALIZED GEOMETRY (CVFF FORCEFIELD) RMSD BONDS (A): 0.0260 ( 0.0000) RMSD ANGLES (DEG): 0.0621 (0.0001) RMSD IMPROPERS (DEG): 0.0485 ( 0.0025) HEAVY ATOM RMS DEVIATIONS OF AVERAGE, MINIMIZED STRUCTURE FROM BEST- FIT SUPERPOSITION OF THE 38 FINAL STRUCTURES RMSD ALL RNA + GENTAMICIN (A): 0.89

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Sample preparation

Sample conditionsIonic strength: 10 mM SODIUM PHOSPHATE / pH: 6.4 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITY+ 500VarianUNITY+ 5005001
Bruker DMX750BrukerDMX7507502

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Processing

NMR software
NameDeveloperClassification
DiscoverBIOSYMrefinement
NMR ARCHITECTstructure solution
DiscoverBIOSYMstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 38 / Conformers submitted total number: 38

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