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- PDB-7qa5: Solution structure of the C terminal domain of MgtC (PA4635) from... -

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Basic information

Entry
Database: PDB / ID: 7qa5
TitleSolution structure of the C terminal domain of MgtC (PA4635) from Pseudomonas aeruginosa
ComponentsProtein MgtC
KeywordsUNKNOWN FUNCTION / Virulence factor
Function / homologyMgtC/SapB/SrpB/YhiD family / MgtC family / membrane => GO:0016020 / plasma membrane / Protein MgtC
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsBarthe, P. / Cohen-Gonsaud, M.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05 France
CitationJournal: To Be Published
Title: Solution structure of the C terminal domain of MgtC (PA4635) from Pseudomonas aeruginosa
Authors: Barthe, P. / Cohen-Gonsaud, M.
History
DepositionNov 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2Jun 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: Protein MgtC


Theoretical massNumber of molelcules
Total (without water)10,8361
Polymers10,8361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein MgtC


Mass: 10836.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ASEAEQRYEVQIVCRAEDEIQVRSLMLHSLGSSDLRLQSLHSEDLDNPAKLEVRAELLGTPEAPAQLERLVSRVSLEKGVSSVRWQVFELAAD
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA4635 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HVF6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-15N TOCSY
133isotropic12D 1H-1H NOESY
143isotropic12D 1H-1H TOCSY
153isotropic12D DQF-COSY
1102isotropic23D HNCA
192isotropic23D HN(CA)CB
182isotropic23D CBCA(CO)NH
172isotropic23D HNCO
162isotropic23D HCACO
1124isotropic13D 1H-13C NOESY aliphatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.4 mM [U-15N] PA4635, 25 mM sodium phosphate, 150 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.4 mM [U-13C; U-15N] PA4635, 25 mM sodium phosphate, 150 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O13C_sample90% H2O/10% D2O
solution30.4 mM [U-13C; U-15N] PA4635, 25 mM sodium phosphate, 150 mM sodium chloride, 2 mM DTT, 100% D2OD2O_sample100% D2O
solution40.4 mM [U-13C; U-15N] PA4635, 25 mM sodium phosphate, 150 mM sodium chloride, 2 mM DTT, 100% D2OC13_D2O_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMPA4635[U-15N]1
25 mMsodium phosphatenatural abundance1
150 mMsodium chloridenatural abundance1
2 mMDTTnatural abundance1
0.4 mMPA4635[U-13C; U-15N]2
25 mMsodium phosphatenatural abundance2
150 mMsodium chloridenatural abundance2
2 mMDTTnatural abundance2
0.4 mMPA4635[U-13C; U-15N]3
25 mMsodium phosphatenatural abundance3
150 mMsodium chloridenatural abundance3
2 mMDTTnatural abundance3
0.4 mMPA4635[U-13C; U-15N]4
25 mMsodium phosphatenatural abundance4
150 mMsodium chloridenatural abundance4
2 mMDTTnatural abundance4
Sample conditionsIonic strength: 150 mM / Label: condition_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III8001equipped with cryoprobe
Bruker AVANCE IIIBrukerAVANCE III7002equipped with cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.6.2Bruker Biospinprocessing
CINDY2.1PAdilla, A.chemical shift assignment
CINDY2.1Padilla, A.peak picking
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 6 / Details: RECOORD procedure
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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