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- PDB-2nc8: NMR structure of the Mycobacterium tuberculosis LppM (Rv2171) pro... -

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Basic information

Entry
Database: PDB / ID: 2nc8
TitleNMR structure of the Mycobacterium tuberculosis LppM (Rv2171) protein folded domain
ComponentsLipoprotein LppM
KeywordsPROTEIN BINDING / TRANSPORT PROTEIN
Function / homology
Function and homology information


peptidoglycan-based cell wall / symbiont-mediated suppression of host innate immune response / lipid binding / extracellular region / membrane
Similarity search - Function
: / LppM domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
DUF3153 domain-containing protein / Protein LppM
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / distance geometry, simulated annealing
Model detailslowest energy, model1
AuthorsBarthe, P. / Cohen-Gonsaud, M.
CitationJournal: Structure / Year: 2016
Title: Mycobacterium tuberculosis LppM Displays an Original Structure and Domain Composition Linked to a Dual Localization.
Authors: Barthe, P. / Veyron-Churlet, R. / de Visch, A. / Gilleron, M. / Saliou, J.M. / Tomavo, S. / Nigou, J. / Brodin, P. / Cohen-Gonsaud, M.
History
DepositionMar 22, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref / struct_ref_seq_dif
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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
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: Lipoprotein LppM


Theoretical massNumber of molelcules
Total (without water)19,4171
Polymers19,4171
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 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Lipoprotein LppM / Lipoprotein lppM / LppM / Uncharacterized protein


Mass: 19417.467 Da / Num. of mol.: 1 / Fragment: residues 26-185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: lppM, AFL40_2254, BN1213_00992, BN1303_00406, ERS007661_00910, ERS007663_00966, ERS007665_02632, ERS007670_01654, ERS007672_03318, ERS007679_00953, ERS007681_03123, ERS007688_03112, ERS007720_ ...Gene: lppM, AFL40_2254, BN1213_00992, BN1303_00406, ERS007661_00910, ERS007663_00966, ERS007665_02632, ERS007670_01654, ERS007672_03318, ERS007679_00953, ERS007681_03123, ERS007688_03112, ERS007720_03717, ERS007722_01662, ERS013447_03488, ERS013471_03169, ERS023446_03335, ERS024213_03999, ERS027644_02995, ERS027653_02310, ERS027656_02172, ERS027666_01329, ERS031493_03859, ERS031537_04052, ERS075357_01597, ERS075361_03109, ERS075387_02172, ERS124361_03770, IQ38_09230, IQ40_08885, IQ42_08970, IQ45_08850, IQ47_08830, IQ48_08865, IU12_09440, IU13_08950, IU16_08915, IU17_08865, T209_08835
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: A0A045INR3, UniProt: O53505*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
1213D 1H-15N NOESY
1313D 1H-15N TOCSY
1423D HNCA
1523D HN(COCA)CB
1623D HN(CA)CB
1723D HNCO
1823D HN(CA)CO
1923D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM [U-100% 15N] protein, 25 mM sodium phosphate, 150 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.9 mM [U-100% 13C; U-100% 15N] protein, 25 mM sodium phosphate, 150 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMentity-1[U-100% 15N]1
25 mMsodium phosphate-21
150 mMsodium chloride-31
0.9 mMentity-4[U-100% 13C; U-100% 15N]2
25 mMsodium phosphate-52
150 mMsodium chloride-62
Sample conditionsIonic strength: 150 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
Gifa4.44Delsucprocessing
CINDY1.9Padilladata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1 / Details: DGSA-distance geometry simulated annealing
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 30

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