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- PDB-2lqj: Solution structure of the C-terminal domain of the MgtC protein f... -

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Basic information

Entry
Database: PDB / ID: 2lqj
TitleSolution structure of the C-terminal domain of the MgtC protein from Mycobacterium tuberculosis
ComponentsMg2+ transport protein
KeywordsHYDROLASE / tuberculosis / ACT domain / membrane protein / regulation
Function / homology
Function and homology information


cellular response to magnesium starvation / plasma membrane
Similarity search - Function
MgtC/SapB/SrpB/YhiD family / : / : / MgtC family / MGTC/SAPB C-terminal domain / ACT domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Mg2+ transport protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsYang, M. / Yang, Y. / Labesse, G. / Blanc-Potard, A.
CitationJournal: J.Bacteriol. / Year: 2012
Title: The C-Terminal Domain of the Virulence Factor MgtC Is a Divergent ACT Domain.
Authors: Yang, Y. / Labesse, G. / Carrere-Kremer, S. / Esteves, K. / Kremer, L. / Cohen-Gonsaud, M. / Blanc-Potard, A.B.
History
DepositionMar 7, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Jun 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 1.3May 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: Mg2+ transport protein


Theoretical massNumber of molelcules
Total (without water)10,4151
Polymers10,4151
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Mg2+ transport protein / POSSIBLE Mg2+ TRANSPORT P-TYPE ATPASE C MGTC


Mass: 10414.767 Da / Num. of mol.: 1 / Fragment: UNP residues 141-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37rv / Gene: mgtC, MT1859, Rv1811 / Production host: Escherichia coli (E. coli) / References: UniProt: O07221, EC: 3.6.3.1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H NOESY
1312D 1H-1H TOCSY
1423D HNCO
1523D HNCA
1623D CBCA(CO)NH
1713D 1H-15N NOESY
1813D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
20.3 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMentity-1[U-100% 15N]1
0.3 mMentity-2[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 0.11 / pH: 4.6 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges, and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1188 / NOE intraresidue total count: 240 / NOE long range total count: 380 / NOE medium range total count: 210 / NOE sequential total count: 358 / Protein chi angle constraints total count: 17 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 69 / Protein psi angle constraints total count: 66
NMR representativeSelection criteria: closest to the average
NMR ensembleAverage torsion angle constraint violation: 2.209 ° / Conformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 15 / Maximum lower distance constraint violation: 0.2 Å / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.3 Å / Torsion angle constraint violation method: RECORD SCRIPTS
NMR ensemble rmsDistance rms dev: 0.0178 Å / Distance rms dev error: 0.012 Å

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