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- PDB-2kg7: Structure and features of the complex formed by the tuberculosis ... -

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Basic information

Entry
Database: PDB / ID: 2kg7
TitleStructure and features of the complex formed by the tuberculosis virulence factors Rv0287 and Rv0288
Components
  • ESAT-6-like protein esxH
  • Uncharacterized protein esxG (PE family protein)
KeywordsUNKNOWN FUNCTION / Protein complex
Function / homology
Function and homology information


Inhibition of membrane repair / : / phagocytic vesicle lumen / Prevention of phagosomal-lysosomal fusion / extracellular region / metal ion binding / cytosol
Similarity search - Function
ESAT-6-like superfamily / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / ESAT-6-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ESAT-6-like protein EsxG / ESAT-6-like protein EsxH / ESAT-6-like protein EsxH
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 28
AuthorsIlghari, D. / Kirsty, L.L. / Waters, L.C. / Veverka, V.L. / Philip, R.S. / Carr, M.D.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Solution structure of the M. tuberculosis EsxG-EsxH complex: functional implications and comparisons with other M. tuberculosis Esx family complexes
Authors: Ilghari, D. / Lightbody, K.L. / Veverka, V. / Waters, L.C. / Muskett, F.W. / Renshaw, P.S. / Carr, M.
History
DepositionMar 6, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein esxG (PE family protein)
B: ESAT-6-like protein esxH


Theoretical massNumber of molelcules
Total (without water)20,2702
Polymers20,2702
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)30 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Uncharacterized protein esxG (PE family protein)


Mass: 9785.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: esxG, MT0300, Rv0287 / Plasmid: pLeics-01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O53692
#2: Protein ESAT-6-like protein esxH / 10 kDa antigen CFP7 / CFP-7 / Low molecular weight protein antigen 7 / Protein TB10.4


Mass: 10483.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: esxH, cfp7, Rv0288, MT0301, MTV035.16 / Plasmid: pLeics-01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A568, UniProt: P9WNK3*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1372D 1H-1H TOCSY
1472D 1H-1H NOESY
1513D 1H-15N NOESY
1613D 1H-15N TOCSY
1733D (H)CCH-TOCSY
1833D 1H-13C NOESY
1953D HNCA
11053D HN(CA)CB
11153D CBCA(CO)NH
1125TROSY HN(CO)CA
11322D 1H-15N HSQC
11442D 1H-13C HSQC
11523D 1H-15N NOESY
11623D 1H-15N TOCSY
11743D (H)CCH-COSY
11843D 1H-13C NOESY
11963D HNCA
12063D HN(CA)CB
12163D CBCA(CO)NH
1226TROSY HN(CO)CA

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7-1mM [U-98% 15N] Labelled Rv0287. unlabelled Rv0288, Sodium phosphate, NaCl, PMSF, Sodium Azide-1, 90% H2O/10% D2O90% H2O/10% D2O
20.7-1mM [U-98% 15N] Labelled Rv0288. unlabelled Rv0287, Sodium phosphate, NaCl, PMSF, Sodium Azide-2, 90% H2O/10% D2O90% H2O/10% D2O
30.7-1mM [U-99% 13C] Labelled Rv0287. unlabelled Rv0288, Sodium phosphate, NaCl, PMSF, Sodium Azide-3, 100% D2O100% D2O
40.7-1mM [U-99% 13C] Labelled Rv0288. unlabelled Rv0287, Sodium phosphate, NaCl, PMSF, Sodium Azide-4, 100% D2O100% D2O
50.7-1mM [U-99% 13C; U-98% 15N] Labelled Rv0287. unlabelled Rv0288, Sodium phosphate, NaCl, PMSF, Sodium Azide-5, 90% H2O/10% D2O90% H2O/10% D2O
60.7-1mM [U-99% 13C; U-98% 15N] Labelled Rv0288. unlabelled Rv0287, Sodium phosphate, NaCl, PMSF, Sodium Azide-6, 90% H2O/10% D2O90% H2O/10% D2O
70.7-1mM Unlabelled Unlabelled Rv0287. unlabelled Rv0288, Sodium phosphate, NaCl, PMSF, Sodium Azide-7, 100% D2O100% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMLabelled Rv0287. unlabelled Rv0288, Sodium phosphate, NaCl, PMSF, Sodium Azide-1[U-98% 15N]0.7-11
mMLabelled Rv0288. unlabelled Rv0287, Sodium phosphate, NaCl, PMSF, Sodium Azide-2[U-98% 15N]0.7-12
mMLabelled Rv0287. unlabelled Rv0288, Sodium phosphate, NaCl, PMSF, Sodium Azide-3[U-99% 13C]0.7-13
mMLabelled Rv0288. unlabelled Rv0287, Sodium phosphate, NaCl, PMSF, Sodium Azide-4[U-99% 13C]0.7-14
mMLabelled Rv0287. unlabelled Rv0288, Sodium phosphate, NaCl, PMSF, Sodium Azide-5[U-99% 13C; U-98% 15N]0.7-15
mMLabelled Rv0288. unlabelled Rv0287, Sodium phosphate, NaCl, PMSF, Sodium Azide-6[U-99% 13C; U-98% 15N]0.7-16
mMUnlabelled Rv0287. unlabelled Rv0288, Sodium phosphate, NaCl, PMSF, Sodium Azide-7Unlabelled0.7-17
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Topspin 2.0Bruker Biospincollection
TopSpinBruker Topspin 2.0Bruker Biospinprocessing
Sparky3.11Goddardchemical shift assignment
Sparky3.11Goddardpeak picking
ProcheckNMRLaskowski, MacArthurdata analysis
CYANAGuntert, Mumenthaler, Wuthrichstructure solution
CYANAGuntert, Mumenthaler, Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 30

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