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- PDB-1krt: SOLUTION STRUCTURE OF THE ANTICODON BINDING DOMAIN OF ESCHERICHIA... -

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Basic information

Entry
Database: PDB / ID: 1krt
TitleSOLUTION STRUCTURE OF THE ANTICODON BINDING DOMAIN OF ESCHERICHIA COLI LYSYL-TRNA SYNTHETASE AND STUDIES OF ITS INTERACTIONS WITH TRNA-LYS
ComponentsLYSYL-TRNA SYNTHETASE (PRODUCT OF LYSS GENE)
KeywordsAMINOACYL-TRNA SYNTHETASE
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / ligase activity / tRNA binding / magnesium ion binding / protein homodimerization activity / ATP binding / membrane / cytosol
Similarity search - Function
Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. ...Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR
AuthorsCommans, S. / Dardel, F.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Solution structure of the anticodon-binding domain of Escherichia coli lysyl-tRNA synthetase and studies of its interaction with tRNA(Lys).
Authors: Commans, S. / Plateau, P. / Blanquet, S. / Dardel, F.
#1: Journal: Nucleic Acids Res. / Year: 1990
Title: Homology of Lyss and Lysu, the Two Escherichia Coli Genes Encoding Distinct Lysyl-tRNA Synthetase Species
Authors: Leveque, F. / Plateau, P. / Dessen, P. / Blanquet, S.
History
DepositionJun 9, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSYL-TRNA SYNTHETASE (PRODUCT OF LYSS GENE)


Theoretical massNumber of molelcules
Total (without water)13,5441
Polymers13,5441
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: LEU 104 - PRO 105 MODEL 8 OMEGA = 244.24 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)9 / -
Representative

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Components

#1: Protein LYSYL-TRNA SYNTHETASE (PRODUCT OF LYSS GENE)


Mass: 13544.372 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM101TR / Description: PTRC99A (IPTG-INDUCIBLE LAC PROMOTER) / Gene: LYSS CODONS 40 - 149 / Plasmid: PTRC-ND / Gene (production host): LYSS CODONS 40 - 149 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8N3, lysine-tRNA ligase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 9

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