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- PDB-2lw3: Solution structure of the soluble domain of MmpS4 from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 2lw3
TitleSolution structure of the soluble domain of MmpS4 from Mycobacterium tuberculosis
ComponentsPutative membrane protein mmpS4
KeywordsMEMBRANE PROTEIN / MmpS4 / soluble domain / Mycobacterium tuberculosis
Function / homology
Function and homology information


: / membrane => GO:0016020 / plasma membrane
Similarity search - Function
MmpS1-5, C-terminal soluble domain / Transport accessory protein MmpS / Transport accessory protein MmpS, C-terminal / Mycobacterium membrane protein / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Siderophore export accessory protein MmpS4 / Siderophore export accessory protein MmpS4
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model16
AuthorsXi, Z. / Sun, P. / Wang, W. / Lai, C. / Wu, F. / Tian, C.
CitationJournal: Plos Pathog. / Year: 2013
Title: Discovery of a Siderophore Export System Essential for Virulence of Mycobacterium tuberculosis
Authors: Wells, R.M. / Jones, C.M. / Xi, Z. / Speer, A. / Danilchanka, O. / Doornbos, K.S. / Sun, P. / Wu, F. / Tian, C. / Niederweis, M.
History
DepositionJul 19, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative membrane protein mmpS4


Theoretical massNumber of molelcules
Total (without water)9,7261
Polymers9,7261
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)20 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative membrane protein mmpS4 / PGB14T-X


Mass: 9725.859 Da / Num. of mol.: 1 / Fragment: the soluble domain, UNP residues 52-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mmpS4 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A5K2, UniProt: P9WJS9*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11023D 1H-15N NOESY
11133D 1H-13C NOESY
11213D (H)CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2-0.5mM [U-100% 13C; U-100% 15N] MmpS4-1, 2mM DTT-2, 50mM sodium phosphate-3, 90% H2O/10% D2O90% H2O/10% D2O
20.2-0.5mM [U-100% 15N] MmpS4-4, 2mM DTT-5, 50mM sodium phosphate-6, 90% H2O/10% D2O90% H2O/10% D2O
30.2-0.5mM [U-100% 13C; U-100% 15N] MmpS4-7, 2mM DTT-8, 50mM sodium phosphate-9, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMMmpS4-1[U-100% 13C; U-100% 15N]0.2-0.51
2 mMDTT-21
50 mMsodium phosphate-31
mMMmpS4-4[U-100% 15N]0.2-0.52
2 mMDTT-52
50 mMsodium phosphate-62
mMMmpS4-7[U-100% 13C; U-100% 15N]0.2-0.53
2 mMDTT-83
50 mMsodium phosphate-93
Sample conditionsIonic strength: 0.108 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA7002
Bruker AvanceBrukerAVANCE8503

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Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificdata analysis
SparkyGoddardpeak picking
SparkyGoddarddata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20 / Representative conformer: 16

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