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- PDB-7n87: Solution NMR structure of peptidase domain from Clostridium therm... -

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Basic information

Entry
Database: PDB / ID: 7n87
TitleSolution NMR structure of peptidase domain from Clostridium thermocellum PCAT1
ComponentsABC-type bacteriocin transporter
KeywordsPEPTIDE BINDING PROTEIN / C39 peptidase domain
Function / homology
Function and homology information


ABC-type bacteriocin transporter activity / ATPase-coupled lipid transmembrane transporter activity / cysteine-type peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding / membrane
Similarity search - Function
Peptidase C39, ABC-type bacteriocin transporter / Peptidase C39 family / Peptidase C39, bacteriocin processing / Peptidase family C39 domain profile. / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter ...Peptidase C39, ABC-type bacteriocin transporter / Peptidase C39 family / Peptidase C39, bacteriocin processing / Peptidase family C39 domain profile. / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ABC-type bacteriocin transporter
Similarity search - Component
Biological speciesHungateiclostridium thermocellum (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsBhattacharya, S. / Palillo, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1P41GM118302-01A1 United States
CitationJournal: Protein Sci. / Year: 2022
Title: Structural and dynamic studies of the peptidase domain from Clostridium thermocellum PCAT1.
Authors: Bhattacharya, S. / Palillo, A.
History
DepositionJun 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 15, 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: ABC-type bacteriocin transporter


Theoretical massNumber of molelcules
Total (without water)16,6351
Polymers16,6351
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein ABC-type bacteriocin transporter


Mass: 16635.389 Da / Num. of mol.: 1 / Mutation: C24A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hungateiclostridium thermocellum (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria)
Strain: ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372
Gene: Cthe_0534 / Plasmid: pMSCG20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3) RIL / References: UniProt: A3DCU1

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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
121isotropic22D 1H-13C HSQC aliphatic
131isotropic22D 1H-13C HSQC aromatic
141isotropic23D HNCO
151isotropic23D HNCA
1101isotropic23D CBCA(CO)NH
191isotropic23D HN(CA)CB
181isotropic23D HN(CO)CA
171isotropic23D HBHA(CO)NH
161isotropic23D (H)CCH-TOCSY
1121isotropic23D C(CO)NH
1111isotropic23D H(CCO)NH
1141isotropic13D 1H-13C NOESY aliphatic
1131isotropic13D 1H-13C NOESY aromatic
1151isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 675 uM [U-100% 13C; U-100% 15N] C39 peptidase domain, 50 uM sodium phosphate, 150 uM sodium chloride, 5 mM DTT, 50 mM PBS buffer, 95% H2O/5% D2O
Details: 50 mM PBS buffer, pH 7.0, 5 mM DTT / Label: 15N/13C-labeled Sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
675 uMC39 peptidase domain[U-100% 13C; U-100% 15N]1
50 uMsodium phosphatenatural abundance1
150 uMsodium chloridenatural abundance1
5 mMDTTnatural abundance1
50 mMPBS buffernatural abundance1
Sample conditionsIonic strength: 150 mM NaCl mM / Label: condition_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE900.031TCI CryoProbe
Bruker AVANCE III HDBrukerAVANCE III HD800.232TCI CryoProbe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1, 3.5Bruker Biospincollection
TopSpin2.1, 3.6Bruker Biospinprocessing
CARA1.5Keller and Wuthrichchemical shift assignment
CARA1.5Keller and Wuthrichpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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