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- PDB-6g5s: Solution structure of the TPR domain of the cell division coordin... -

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Basic information

Entry
Database: PDB / ID: 6g5s
TitleSolution structure of the TPR domain of the cell division coordinator, CpoB
ComponentsCell division coordinator CpoB
KeywordsCELL CYCLE / PBP1B / Cell division coordinator / E. coli / transpeptidase regulator
Function / homology
Function and homology information


protein trimerization / FtsZ-dependent cytokinesis / outer membrane-bounded periplasmic space / cell division / protein-containing complex
Similarity search - Function
Cell division coordinator CpoB, C-terminal / YbgF, trimerisation domain / Cell division coordinator CpoB / TolA binding protein trimerisation / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Cell division coordinator CpoB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailsCell division coordinator
AuthorsSimorre, J.P. / Maya Martinez, R.C. / Bougault, C. / Vollmer, W. / Egan, A.
Funding support France, United Kingdom, 3items
OrganizationGrant numberCountry
French National Research AgencyANR-14-JAMR-0003 France
Wellcome Trust101824/Z/13/Z United Kingdom
French National Research AgencyANR-10-INSB-05-02 France
CitationJournal: Mol. Microbiol. / Year: 2018
Title: Induced conformational changes activate the peptidoglycan synthase PBP1B.
Authors: Egan, A.J.F. / Maya-Martinez, R. / Ayala, I. / Bougault, C.M. / Banzhaf, M. / Breukink, E. / Vollmer, W. / Simorre, J.P.
History
DepositionMar 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division coordinator CpoB


Theoretical massNumber of molelcules
Total (without water)16,1521
Polymers16,1521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8610 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 75020
RepresentativeModel #1lowest energy

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Components

#1: Protein Cell division coordinator CpoB


Mass: 16152.112 Da / Num. of mol.: 1 / Fragment: Cell division protein CpoB (101-225)
Source method: isolated from a genetically manipulated source
Details: TPR domain of E. coli CpoB (residues 139-263)
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: cpoB, ybgF, b0742, JW0732 / Plasmid: pAJFE01 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P45955

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic23D HNCO
131isotropic23D HN(CA)CO
141isotropic33D BESTROSY-HN(CA)CB
151isotropic33D BESTROSY-HN(CO)CACB
161isotropic22D 1H-13C HSQC aliphatic
171isotropic22D 1H-13C HSQC aromatic
181isotropic33D (H)CCH-TOCSY
191isotropic33D (H)CCH-TOCSY
1101isotropic43D 1H-15N NOESY
1111isotropic33D 1H-13C NOESY aliphatic
1121isotropic33D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution / Contents: 2 mM [U-13C; U-15N] CpoB, 90% H2O and 10% D2O
Details: TPR domain of CpoB (resiudes 139-263) uniformly 13C,15N-labeled
Label: 15N-13C-CpoB / Solvent system: 90% H2O and 10% D2O
SampleConc.: 2 mM / Component: CpoB / Isotopic labeling: [U-13C; U-15N]
Sample conditionsDetails: 10 mM Tris/HCl 200 mM NaCl / Ionic strength: 200 mM / Label: 15N-13C-CpoB / pH: 7.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7002
Bruker AVANCEBrukerAVANCE8503
Bruker US2BrukerUS29504

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Rieping W., Habeck M., Bardiaux B., Bernard A , Nilges M.structure calculation
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CcpNmr Analysis2.4CCPNchemical shift assignment
TALOS+Yang Shen, Frank Delaglio, Gabriel Cornilescu, and Ad Baxdata analysis
UNIO2.0.2Torsten Herrmannstructure calculation
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 / Conformers calculated total number: 750 / Conformers submitted total number: 20

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