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- PDB-3zgp: NMR structure of the catalytic domain from E. faecium L,D- transp... -

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Basic information

Entry
Database: PDB / ID: 3zgp
TitleNMR structure of the catalytic domain from E. faecium L,D- transpeptidase acylated by ertapenem
ComponentsERFK/YBIS/YCFS/YNHG
KeywordsTRANSFERASE / TRANSPEPTIDATION / PEPTIDOGLYCAN BIOSYNTHESIS / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


peptidoglycan biosynthetic process / transferase activity / membrane
Similarity search - Function
Putative peptidoglycan binding domain / L,D-transpeptidase central domain-like superfamily / Putative peptidoglycan binding domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-1RG / ErfK/YbiS/YcfS/YnhG family protein
Similarity search - Component
Biological speciesENTEROCOCCUS FAECIUM (bacteria)
MethodSOLUTION NMR / ARIA2.3
AuthorsLecoq, L. / Triboulet, S. / Dubee, V. / Bougault, C. / Hugonnet, J.E. / Arthur, M. / Simorre, J.P.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: The Structure of Enterococcus Faecium L,D---Transpeptidase Acylated by Ertapenem Provides Insight Into the Inactivation Mechanism.
Authors: Lecoq, L. / Triboulet, S. / Dubee, V. / Bougault, C. / Hugonnet, J.E. / Arthur, M. / Simorre, J.P.
History
DepositionDec 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Feb 12, 2014Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other
Revision 1.3Jan 24, 2018Group: Data collection / Database references / Category: citation / pdbx_nmr_spectrometer
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 2.0Jun 14, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ERFK/YBIS/YCFS/YNHG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0502
Polymers14,5721
Non-polymers4781
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1700TOTAL ENERGY
RepresentativeModel #1

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Components

#1: Protein ERFK/YBIS/YCFS/YNHG / LDTFM-ERTAPENEM


Mass: 14572.148 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 341-466
Source method: isolated from a genetically manipulated source
Details: ERTAPENEM ANTIBIOTIC IS COVALENTLY LINKED TO THE CYSTEINE OF THE ENZYME.
Source: (gene. exp.) ENTEROCOCCUS FAECIUM (bacteria) / Plasmid: PETTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3Y185, EC: 2.3.2.12
#2: Chemical ChemComp-1RG / (4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid / ERTAPENEM, bound form PRE-ISOMERIZED / Ertapenem


Mass: 477.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N3O7S / Comment: medication, antibiotic*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-15N-HSQC
1211H-13C-HSQC CENTERED ON ALIPHATICS
1311H-15N-HMQC DETECTING 2J
1413J COUPLINGS IN HISTIDINES IMIDAZOLE RING
151HSQC DETECTING 1J COUPLING IN HISTIDINES IMIDAZOLE RING
161HN(CA)CB
171HNCO
1813D-15N-NOESY-HSQC
1913D-13C-NOESY-HSQC CENTERED ON ALIPHATICS
11011H-13C- HSQC CENTERED ON AROMATICS
11113D-13C-NOESY-HSQC CENTERED ON AROMATICS
112113C-15N-FILTERED NOESY
NMR detailsText: THE 20 NMR STRUCTURES WERE DETERMINED USING TRIPLE- RESONANCE NMR SPECTROSCOPY ON A 13C, 15N-LABELED LDTFM SAMPLE INCUBATED WITH 1 EQUIVALENT OF ERTAPENEM ANTIBIOTIC. THESE STRUCTURES WERE ...Text: THE 20 NMR STRUCTURES WERE DETERMINED USING TRIPLE- RESONANCE NMR SPECTROSCOPY ON A 13C, 15N-LABELED LDTFM SAMPLE INCUBATED WITH 1 EQUIVALENT OF ERTAPENEM ANTIBIOTIC. THESE STRUCTURES WERE REFINED IN WATER WITHIN CNS ARIA.

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Sample preparation

Details
Solution-IDContents
110% WATER/90% D2O
2100% D2O
Sample conditionsIonic strength: 300 mM / pH: 6.4 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent Direct DriveAgilentDirect Drive6001
Bruker Direct DriveBrukerDirect Drive6002
Agilent Direct DriveAgilentDirect Drive6003
Agilent Direct DriveAgilentDirect Drive6004
Agilent Direct DriveAgilentDirect Drive6005
Agilent Direct DriveAgilentDirect Drive8006
Bruker AVANCEBrukerAVANCE9507
Agilent Direct DriveAgilentDirect Drive8008
Agilent Direct DriveAgilentDirect Drive8009

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Processing

NMR software
NameVersionDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
UNIO10structure solution
TALOSstructure solution
CcpNmr AnalysisANALYSISstructure solution
RefinementMethod: ARIA2.3 / Software ordinal: 1
NMR ensembleConformer selection criteria: TOTAL ENERGY / Conformers calculated total number: 1700 / Conformers submitted total number: 20

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