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- PDB-2lt2: NMR structure of BA42 protein from the psychrophilic bacteria Biz... -

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Basic information

Entry
Database: PDB / ID: 2lt2
TitleNMR structure of BA42 protein from the psychrophilic bacteria Bizionia argentinensis sp. nov.
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / BA42 / Psychrophilic
Function / homologyDiaminopimelate Epimerase; Chain A, domain 1 - #50 / TPM domain / TPM domain / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / metal ion binding / membrane / Alpha Beta / TPM domain-containing protein
Function and homology information
Biological speciesBizionia argentinensis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsCicero, D.O. / Smal, C. / Aran, M. / Gallo, M. / Pellizza, L.
Citation
Journal: To be Published
Title: NMR structure of BA42 protein from the psychrophilic bacteria Bizionia argentinensis sp. nov.
Authors: Smal, C. / Aran, M. / Lanzarotti, E. / Papouchado, M. / Foti, M. / Marti, M. / Coria, S. / Vazquez, S. / Bercovich, A. / Mac Cormack, W. / Turjanski, A. / Gallo, M. / Cicero, D.
#1: Journal: Biomol.Nmr Assign. / Year: 2011
Title: (1)H, (15)N and (13)C chemical shift assignments of the BA42 protein of the psychrophilic bacteria Bizionia argentinensis sp. nov.
Authors: Smal, C. / Aran, M. / Lanzarotti, E. / Papouchado, M. / Foti, M. / Marti, M.A. / Coria, S.H. / Vazquez, S.C. / Bercovich, A. / Mac Cormack, W.P. / Turjanski, A.G. / Gallo, M. / Cicero, D.O.
History
DepositionMay 10, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)16,4991
Polymers16,4991
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)20 / 6000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative uncharacterized protein


Mass: 16498.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bizionia argentinensis (bacteria) / Strain: JUB59 / Gene: BZARG_1551 / Plasmid: pDEST527 / Production host: Escherichia coli (E. coli) / References: UniProt: G2EA45

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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 CBCA(CO)NH
1313D HNCO
1413D HNCA
1513D HN(CO)CA
1613D HBHA(CO)NH
1713D 1H-15N NOESY
1813D 1H-15N TOCSY
1913D 1H-13C NOESY
11013D 1H-13C NOESY aromatic
11113D 1H-13C NOESY aliphatic

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] BA42 protein, 50 mM TrisHCl, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMBA42 protein-1[U-100% 13C; U-100% 15N]1
50 mMTrisHCl-21
Sample conditionsIonic strength: 0.1 / pH: 7.5 / Pressure: ambient / Temperature: 301.5 K

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NMR measurement

NMR spectrometerType: Bruker Ultrashield / Manufacturer: Bruker / Model: Ultrashield / Field strength: 600 MHz

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Processing

NMR software
NameClassification
X-PLORstructure solution
X-PLORrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 6000 / Conformers submitted total number: 20

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