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- PDB-1yub: SOLUTION STRUCTURE OF AN RRNA METHYLTRANSFERASE (ERMAM) THAT CONF... -

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Basic information

Entry
Database: PDB / ID: 1yub
TitleSOLUTION STRUCTURE OF AN RRNA METHYLTRANSFERASE (ERMAM) THAT CONFERS MACROLIDE-LINCOSAMIDE-STREPTOGRAMIN ANTIBIOTIC RESISTANCE, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsRRNA METHYLTRANSFERASE
KeywordsMETHYLTRANSFERASE / ERM / ERMAM / MLS ANTIBIOTICS / RRNA
Function / homology
Function and homology information


23S rRNA (adenine2085-N6)-dimethyltransferase / 23S rRNA (adenine(2085)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / response to antibiotic / RNA binding
Similarity search - Function
rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Helicase, Ruva Protein; domain 3 ...rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
rRNA adenine N-6-methyltransferase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodSOLUTION NMR / DG, SA
AuthorsYu, L. / Petros, A.M. / Schnuchel, A. / Zhong, P. / Severin, J.M. / Walter, K. / Holzman, T.F. / Fesik, S.W.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Solution structure of an rRNA methyltransferase (ErmAM) that confers macrolide-lincosamide-streptogramin antibiotic resistance.
Authors: Yu, L. / Petros, A.M. / Schnuchel, A. / Zhong, P. / Severin, J.M. / Walter, K. / Holzman, T.F. / Fesik, S.W.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Erratum. Solution Structure of an Rrna Methyltransferase (Ermam) that Confers Macrolide-Lincosamide-Streptogramin Antibiotic Resistance
Authors: Yu, L. / Petros, A.M. / Schnuchel, A. / Zhong, P. / Severin, J.M. / Walter, K. / Holzman, T.F. / Fesik, S.W.
History
DepositionMar 4, 1997Processing site: BNL
Revision 1.0Mar 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RRNA METHYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)28,8631
Polymers28,8631
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 17LOWEST ENERGY AND LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein RRNA METHYLTRANSFERASE / ERMAM


Mass: 28862.568 Da / Num. of mol.: 1 / Mutation: I75T, S100N, H118R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria)
Strain: 5728, A CLINICAL ISOLATE FROM ABBOTT CULTURE COLLECTION
Cell line: BL21 / Gene: ERM / Plasmid: PET-24(+) / Species (production host): Escherichia coli / Gene (production host): ERM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P21236, EC: 2.1.1.48

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D
1213D
1314D NMR

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Sample preparation

Sample conditionsIonic strength: 50 mM SODIUM PHOSPHATE, 100 mM NACL / pH: 6.5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX500BrukerDMX5005001
Bruker AMX600BrukerAMX6006002
Bruker DRX800BrukerDRX8008003

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: DG, SA / Software ordinal: 1
Details: THE TOTAL NUMBER OF DISTANCE RESTRAINTS USED WAS 3259. THE TOTAL NUMBER OF TORSIONAL RESTRAINTS USED WAS 63.
NMR ensembleConformer selection criteria: LOWEST ENERGY AND LEAST RESTRAINT VIOLATION
Conformers calculated total number: 17 / Conformers submitted total number: 1

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