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- PDB-1e0g: LYSM Domain from E.coli MLTD -

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Basic information

Entry
Database: PDB / ID: 1e0g
TitleLYSM Domain from E.coli MLTD
ComponentsMembrane-bound lytic murein transglycosylase D
KeywordsHYDROLASE / CELL WALL / GLYCOSIDASE / LIPOPROTEIN / OUTER MEMBRANE / MULTIGENE FAMILY
Function / homology
Function and homology information


lytic endotransglycosylase activity / : / lytic transglycosylase activity / positive regulation of oxidoreductase activity / peptidoglycan metabolic process / cell wall organization / lyase activity / membrane / plasma membrane
Similarity search - Function
Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. ...Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Lysozyme-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Peptidoglycan lytic exotransglycosylase / Membrane-bound lytic murein transglycosylase D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / SA
AuthorsBateman, A. / Bycroft, M.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: The Structure of a Lysm Domain from E.Coli Membrane Bound Lytic Murein Transglycosylase D (Mltd)
Authors: Bateman, A. / Bycroft, M.
#1: Journal: Can.J.Microbiol. / Year: 1994
Title: Cloning, Molecular Characterization, and Expression of the Genes Encoding the Lytic Functions of Lactococcal Bacteriophage-Phi-Lc3; a Dual Lysis System of Modular Design
Authors: Birkeland, N.K.
History
DepositionMar 27, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2000Provider: repository / Type: Initial release
SupersessionNov 5, 2003ID: 1E01
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 25, 2019Group: Data collection / Database references ...Data collection / Database references / Other / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / pdbx_database_status / pdbx_entity_src_syn / pdbx_nmr_software / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _pdbx_database_status.status_code_mr / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_nmr_software.name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Membrane-bound lytic murein transglycosylase D


Theoretical massNumber of molelcules
Total (without water)5,4421
Polymers5,4421
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein/peptide Membrane-bound lytic murein transglycosylase D


Mass: 5442.219 Da / Num. of mol.: 1 / Fragment: LYSM DOMAIN / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
References: UniProt: A0A2Z2J5F1, UniProt: P0AEZ7*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED MTLD LYSM DOMAIN

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Sample preparation

Sample conditionspH: 6.8 / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: SA / Software ordinal: 1 / Details: SA FROM RANDOM COIL STARTING STRUCTURES
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 20

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