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- PDB-4a52: NMR structure of the imipenem-acylated L,D-transpeptidase from Ba... -

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Basic information

Entry
Database: PDB / ID: 4a52
TitleNMR structure of the imipenem-acylated L,D-transpeptidase from Bacillus subtilis
ComponentsPUTATIVE L, D-TRANSPEPTIDASE YKUD
KeywordsTRANSFERASE / PEPTIDOGLYCAN / ANTIBIOTIC RESISTANCE / CYSTEINE PROTEASE
Function / homology
Function and homology information


spore wall / Transferases / peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / sporulation resulting in formation of a cellular spore / glycosyltransferase activity / cell wall organization / regulation of cell shape
Similarity search - Function
Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / : / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / LysM domain superfamily ...Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / : / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / LysM domain superfamily / Lysin motif / LysM domain / LysM domain profile. / LysM domain / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-IM2 / Putative L,D-transpeptidase YkuD
Similarity search - Component
Biological speciesBACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
MethodSOLUTION NMR / ITERATIVE STRUCTURE CALCULATION WITH ARIA2.3
AuthorsLecoq, L. / Simorre, J. / Bougault, C. / Arthur, M. / Hugonnet, J. / Veckerle, C. / Pessey, O.
CitationJournal: Structure / Year: 2012
Title: Dynamics Induced by Beta-Lactam Antibiotics in the Active Site of Bacillus subtilis L,D-Transpeptidase.
Authors: Lecoq, L. / Bougault, C. / Hugonnet, J. / Veckerle, C. / Pessey, O. / Arthur, M. / Simorre, J.P.
History
DepositionOct 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Other
Revision 1.2Jan 15, 2014Group: Database references / Structure summary
Revision 2.0Jan 24, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / citation / database_PDB_caveat / pdbx_nmr_spectrometer
Item: _citation.page_last / _citation.title ..._citation.page_last / _citation.title / _database_PDB_caveat.text / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 2.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_entity_nonpoly.name / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUTATIVE L, D-TRANSPEPTIDASE YKUD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2622
Polymers18,9611
Non-polymers3011
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20STRUCTURE WITH THE LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein PUTATIVE L, D-TRANSPEPTIDASE YKUD / SPORE PROTEIN YKUD / IMIPENEM-LDTBS


Mass: 18960.732 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-164
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PREP4GROESL / References: UniProt: O34816, Transferases
#2: Chemical ChemComp-IM2 / (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form


Mass: 301.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N3O4S / Comment: antibiotic*YM
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11113C-HSQC-NOESY
2211H-15N- HSQC
3311H -13C-HSQC
44113C- HSQC-NOESY METHYL SELECTIVE
55115N-HSQC-NOESY
6611H-15N- HMQC OPTIMIZED FOR IMIDAZOLE RING OF HISTIDINES
771HNCO
881HN(CA)CB
9911H- 13C-HSQC CENTERED ON AROMATICS
1010113C-HSQC-NOESY CENTERED ON AROMATICS
NMR detailsText: THE 20 NMR STRUCTURES WERE DETERMINED USING TRIPLE- RESONANCE NMR SPECTROSCOPY ON A 13C, 15N-LABELED LDTBS SAMPLE INCUBATED WITH 2.5 EQUIVALENTS OF IMIPENEM ANTIBIOTIC. THESE STRUCTURES WERE ...Text: THE 20 NMR STRUCTURES WERE DETERMINED USING TRIPLE- RESONANCE NMR SPECTROSCOPY ON A 13C, 15N-LABELED LDTBS SAMPLE INCUBATED WITH 2.5 EQUIVALENTS OF IMIPENEM ANTIBIOTIC. THESE STRUCTURES WERE REFINED WITH RDCS, AND REFINED IN WATER WITHIN CNS ARIA.

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Sample preparation

DetailsContents: 90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.156.51.0 atm298.0 K
20.156.51.0 atm298.0 K
30.156.51.0 atm298.0 K
40.156.51.0 atm298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE8002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
CNS1.2structure solution
TALOS+ANYstructure solution
UNIO10structure solution
NMRDrawANYstructure solution
NMRPipeANYstructure solution
CcpNmr Analysis2.2structure solution
RefinementMethod: ITERATIVE STRUCTURE CALCULATION WITH ARIA2.3 / Software ordinal: 1 / Details: REFINEMENT IN WATER AFTER 8 ITERATIONS.
NMR ensembleConformer selection criteria: STRUCTURE WITH THE LOWEST ENERGY
Conformers calculated total number: 20 / Conformers submitted total number: 20

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