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- PDB-1nyo: Solution structure of the antigenic TB protein MPT70/MPB70 -

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Basic information

Entry
Database: PDB / ID: 1nyo
TitleSolution structure of the antigenic TB protein MPT70/MPB70
ComponentsImmunogenic protein MPT70
KeywordsIMMUNE SYSTEM / seven-stranded beta-barrel / fasciclin domain / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


extracellular space / extracellular region
Similarity search - Function
FAS1 domain / FAS1 domain / FAS1 domain / FAS1 domain superfamily / Fasciclin domain / FAS1/BIgH3 domain profile. / Four repeated domains in the Fasciclin I family of proteins, present in many other contexts. / Roll / Mainly Beta
Similarity search - Domain/homology
Immunogenic protein MPT70 / Immunogenic protein MPT70
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics with simmulated annealing
AuthorsBloemink, M.J. / Dentten, E. / Hewinson, R.G. / Williamson, R.A. / Carr, M.D. / TB Structural Genomics Consortium (TBSGC)
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Solution structure of the Mycobacterium tuberculosis complex protein MPB70: from tuberculosis pathogenesis to inherited human corneal desease
Authors: Carr, M.D. / Bloemink, M.J. / Dentten, E. / Whelan, A.O. / Gordon, S.V. / Kelly, G. / Frenkiel, T.A. / Hewinson, R.G. / Williamson, R.A.
#1: Journal: J.Biomol.NMR / Year: 2001
Title: Sequence-specific assignment and determination of the secondary structure of the 163-residue M.tuberculosis and M.bovis antigenic protein MPB70
Authors: Bloemink, M.J. / Kemmink, J. / Dentten, E. / Muskett, F.W. / Whelan, A. / Sheikh, A. / Hewinson, G. / Williamson, R.A. / Carr, M.D.
History
DepositionFeb 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunogenic protein MPT70


Theoretical massNumber of molelcules
Total (without water)16,3111
Polymers16,3111
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)38 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Immunogenic protein MPT70 / mycobacterial protein MPT70 / MPB70


Mass: 16311.118 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mpt70/mpb70 / Plasmid: pBluescript KS+ / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P0A668, UniProt: P9WNF5*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 15N-separated NOESY
1233D 13C-separated NOESY
132HNHB
1423D 15N-separated TOCSY (short tmix)
1542D NOESY
1652D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7mM MPB70 U-15N,13C, 20mM phosphate buffer/100mM NaCl90% H2O/10% D2O
21.0mM MPB70 U-15N, 20mM phosphate buffer/100mM NaCl90% H2O/10% D2O
31.0mM MPB70 U-15N,U-13C (except Y,H,F(12C)), 20mM phosphate buffer/100mM NaCl100% D2O
41.0mM MPB70 U-14N,12C, 20mM phosphate buffer/100mM NaCl90% H2O/10% D2O
51.0mM MPB70 U-14N,12C, 20mM phosphate buffer/100mM NaCl100% D2O
Sample conditionsIonic strength: 20mM phosphate/100mM NaCl / pH: 6.0 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVariancollection
NMRPipesgi6xDelaglioprocessing
XEASY1.3.11Bartelsdata analysis
CYANA1.0.3Guentertstructure solution
CYANA1.0.3Guentertrefinement
RefinementMethod: torsion angle dynamics with simmulated annealing / Software ordinal: 1
Details: the solution structures are based on a total of 2892 NOE-derived distance constraints, 98 distance constraints from hydrogen bonds and 35 torsion angle constraints
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: 38

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