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- PDB-2mgv: NMR structure of PASTA domain of PonA2 from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 2mgv
TitleNMR structure of PASTA domain of PonA2 from Mycobacterium tuberculosis
ComponentsBifunctional membrane-associated penicillin-binding protein 1A/1B ponA2
KeywordsPENICILLIN BINDING PROTEIN / PASTA domain
Function / homology
Function and homology information


: / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / response to antibiotic
Similarity search - Function
Trypsin Inhibitor V; Chain A - #20 / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / Transglycosylase / Trypsin Inhibitor V; Chain A / Penicillin-binding protein, transpeptidase ...Trypsin Inhibitor V; Chain A - #20 / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / Transglycosylase / Trypsin Inhibitor V; Chain A / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like / Lysozyme-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Penicillin-insensitive transglycosylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model1
AuthorsCalvanese, L. / Falcigno, L. / Maglione, C. / Marasco, D. / Ruggiero, A. / Squeglia, F. / Berisio, R. / D'Auria, G.
CitationJournal: Biopolymers / Year: 2014
Title: Structural and binding properties of the PASTA domain of PonA2, a key penicillin binding protein from Mycobacterium tuberculosis.
Authors: Calvanese, L. / Falcigno, L. / Maglione, C. / Marasco, D. / Ruggiero, A. / Squeglia, F. / Berisio, R. / D'Auria, G.
History
DepositionNov 11, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional membrane-associated penicillin-binding protein 1A/1B ponA2


Theoretical massNumber of molelcules
Total (without water)6,5781
Polymers6,5781
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 150structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Bifunctional membrane-associated penicillin-binding protein 1A/1B ponA2


Mass: 6578.211 Da / Num. of mol.: 1 / Fragment: PASTA domain (UNP residues 700-764)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: RVBD_3682 / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / References: UniProt: I6YGX2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1223D 1H-15N TOCSY
1323D 1H-15N NOESY
1412D 1H-1H TOCSY
1512D 1H-1H NOESY
1612D DQF-COSY
1733D HNCO
1833D HN(CA)CB
1933D (H)CCH-TOCSY
11033D CBCA(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5-1.6 mM PonA2-PASTA, 10% D2O, 30 mM sodium phosphate, 0.02% sodium azide, 90% phosphate buffer/10% D2O90% phosphate buffer/10% D2O
21.8-1.9 mM [U-100% 15N] PonA2-PASTA, 10% D2O, 30 mM sodium phosphate, 0.02% sodium azide, 90% phosphate buffer/10% D2O90% phosphate buffer/10% D2O
31.3 mM [U-100% 13C; U-100% 15N] PonA2-PASTA, 10% D2O, 30 mM sodium phosphate, 0.02% sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMPonA2-PASTA-11.5-1.61
10 %D2O-21
30 mMsodium phosphate-31
0.02 %sodium azide-41
mMPonA2-PASTA-5[U-100% 15N]1.8-1.92
10 %D2O-62
30 mMsodium phosphate-72
0.02 %sodium azide-82
1.3 mMPonA2-PASTA-9[U-100% 13C; U-100% 15N]3
10 %D2O-103
30 mMsodium phosphate-113
0.02 %sodium azide-123
Sample conditionspH: 6.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.9.0 Beta 3(CARA) Rochus Keller and otherschemical shift assignment
CARA1.9.0 Beta 3(CARA) Rochus Keller and otherspeak picking
CARA1.9.0 Beta 3(CARA) Rochus Keller and othersdata analysis
Sparky3Goddardprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
ProcheckNMRLaskowski and MacArthurstructure validation
PSVSBhattacharya and Montelionestructure validation
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 150 / Conformers submitted total number: 10

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