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- PDB-6qs0: NMR structure of BB_A03, Borrelia burgdorferi outer surface lipop... -

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Basic information

Entry
Database: PDB / ID: 6qs0
TitleNMR structure of BB_A03, Borrelia burgdorferi outer surface lipoprotein
ComponentsPutative outer membrane protein BBA03
KeywordsMEMBRANE PROTEIN / Lipoprotein
Function / homologycell outer membrane / membrane / Putative outer membrane protein BBA03
Function and homology information
Biological speciesBorreliella burgdorferi B31 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsFridmanis, J. / Brangulis, K. / Jaudzems, K.
CitationJournal: Pathogens / Year: 2020
Title: Structural and Functional Analysis of BBA03, Borrelia burgdorferi Competitive Advantage Promoting Outer Surface Lipoprotein.
Authors: Fridmanis, J. / Bobrovs, R. / Brangulis, K. / Tars, K. / Jaudzems, K.
History
DepositionFeb 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative outer membrane protein BBA03


Theoretical massNumber of molelcules
Total (without water)13,7471
Polymers13,7471
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6690 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Putative outer membrane protein BBA03


Mass: 13746.589 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_A03 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q44849

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY aliphatic
131isotropic13D 1H-13C NOESY aromatic
141isotropic13D HNCO
151isotropic13D HNCA
161isotropic13D CBCA(CO)NH

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Sample preparation

DetailsType: solution
Contents: 20 mM sodium phosphate, 50 mM sodium chloride, 0.03 % w/v sodium azide, 1 mM EDTA, 2 mM [U-13C; U-15N] BB_A03, 95% H2O/5% D2O
Label: BB_A03_C13_N15 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
0.03 % w/vsodium azidenatural abundance1
1 mMEDTAnatural abundance1
2 mMBB_A03[U-13C; U-15N]1
Sample conditionsIonic strength: 0.08 M / Ionic strength err: 0.01 / Label: Standard / pH: 6.8 / PH err: 0.1 / Pressure: AMBIENT Pa / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CANDID2.02Herrmann, Guntert and Wuthrichstructure calculation
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
TopSpin3.5Bruker Biospincollection
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: 100 / Conformers submitted total number: 20

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