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- PDB-2hhi: The solution structure of antigen MPT64 from Mycobacterium tuberc... -

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Basic information

Entry
Database: PDB / ID: 2hhi
TitleThe solution structure of antigen MPT64 from Mycobacterium tuberculosis defines a novel class of beta-grasp proteins
ComponentsImmunogenic protein MPT64
KeywordsUNKNOWN FUNCTION / MPT64 / Secreted Antigen / Tuberculosis / Residual Dipolar Coupling / NMR Solution Structure / beta-grasp
Function / homology
Function and homology information


cell wall / zymogen binding / peptidoglycan-based cell wall / cellular response to starvation / extracellular region
Similarity search - Function
: / Fervidobacterium nodosum Rt17-B1 like / Heat-shock cognate protein, ATPase / Domain of unknown function DUF3298 / PdaC/RsiV-like superfamily / Protein of unknown function (DUF3298) / Actin; Chain A, domain 4 / Heat Shock Protein 90 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Immunogenic protein MPT64 / Immunogenic protein MPT64
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / Torsion Angle Dynamics, RDC refinement using CNS 1.1
AuthorsWang, Z. / Potter, B.M. / Gray, A.M. / Sacksteder, K.A. / Geisbrecht, B.V. / Laity, J.H.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: The Solution Structure of Antigen MPT64 from Mycobacterium tuberculosis Defines a New Family of Beta-Grasp Proteins.
Authors: Wang, Z. / Potter, B.M. / Gray, A.M. / Sacksteder, K.A. / Geisbrecht, B.V. / Laity, J.H.
#1: Journal: Protein Expr.Purif. / Year: 2006
Title: Design and optimization of a recombinant system for large-scale production of the MPT64 antigen from Mycobacterium tuberculosis.
Authors: Geisbrecht, B.V. / Nikonenko, B. / Samala, R. / Nakamura, R. / Nacy, C.A. / Sacksteder, K.A.
#2: Journal: J.Biomol.NMR / Year: 2005
Title: NMR assignment of protein Rv1980c from Mycobacterium tuberculosis
Authors: Danahy, J.M. / Potter, B.M. / Geisbrecht, B.V. / Laity, J.H.
History
DepositionJun 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 MPT64


Theoretical massNumber of molelcules
Total (without water)22,3761
Polymers22,3761
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)24 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Immunogenic protein MPT64 / Antigen MPT64


Mass: 22375.855 Da / Num. of mol.: 1 / Fragment: Recombinant form of mature polypeptide
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: mpt64 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A5Q4, UniProt: P9WIN9*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1115N-edited NOESY
121NHSQC
13213C-edited NOESY (aliphatic and aromatic)
143HNCA
153CBCA(CO)NH
163HN(CA)CB
173HNCO
183(HCA)CO(CA)NH (Varian BioPack Software Package)

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Sample preparation

Details
Solution-IDContents
12.0 mM recombinant MPT64 (15N-enriched), saturated d13-MES pH 6.9 with 5% D2O, 0.2 mM DSS, 1mM NaN3
22.0 mM recombinant MPT64 (13C-enriched), saturated d13-MES pH 6.9 with 99% D2O, 0.2 mM DSS, 1mM NaN3
32.0 mM recombinant MPT64 (15N,13C), saturated d13-MES pH 6.9 with 5% D2O, 0.2 mM DSS, 1mM NaN3
Sample conditionsIonic strength: no salt / pH: 6.9 / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenrefinement
NMRPipe97.027.12.56F. Delaglio, S. Grzesiek, G.W. Vuister, G. Zhu, J. Pfeifer, A. Baxprocessing
NMRView5.0.4B.A. Johnson, R.A. Blevinsdata analysis
Module1P. Dosset, J. Hus, M. Blackledgedata analysis
RefinementMethod: Torsion Angle Dynamics, RDC refinement using CNS 1.1
Software ordinal: 1
Details: The initial structures were calculated through TAD protocol of CNS with 3761 NOE-derived distance contraints and 292 dihedral angle restraints. The final structures were refined using JNH ...Details: The initial structures were calculated through TAD protocol of CNS with 3761 NOE-derived distance contraints and 292 dihedral angle restraints. The final structures were refined using JNH and JCaCO Residual Dipolar Coupling (RDC) in Cartesian space with same NOE, dihedral angle restraints and 139 JNH RDCs and 114 JCaCO RDCs from stretched gel.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 24

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