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- PDB-2k32: Truncated AcrA from Campylobacter jejuni for glycosylation studies -

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Basic information

Entry
Database: PDB / ID: 2k32
TitleTruncated AcrA from Campylobacter jejuni for glycosylation studies
ComponentsA
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / nonglycosylated AcrA
Function / homologyRND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / transmembrane transporter activity / Prokaryotic membrane lipoprotein lipid attachment site profile. / membrane / CmeA
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodSOLUTION NMR / simulated annealing
Model detailsStructure an chemical shifts of truncated AcrA from Campylobacter jejuni for glycosylation studies
AuthorsSlynko, V. / Schubert, M. / Numao, S. / Kowarik, M. / Aebi, M. / Allain, F.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: NMR structure determination of a segmentally labeled glycoprotein using in vitro glycosylation.
Authors: Slynko, V. / Schubert, M. / Numao, S. / Kowarik, M. / Aebi, M. / Allain, F.H.
History
DepositionApr 17, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 8, 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: A


Theoretical massNumber of molelcules
Total (without water)12,7481
Polymers12,7481
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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 A


Mass: 12748.244 Da / Num. of mol.: 1
Fragment: Truncated protein (UNP residues: 61-96,118-145,167-210)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: cmeA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8RTE5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Structure an chemical shifts of truncated AcrA from Campylobacter jejuni for glycosylation studies
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-13C HSQC
1312D 1H-1H NOESY
1432D 1H-1H NOESY
1523D HN(CA)CB
1623D HNCA
1723D HN(CO)CA
1832D 1H-15N HSQC
1923D (H)CCH-TOCSY
11023D 1H-13C NOESY
11113D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] AcrA(61-210DD), 50 mM potassium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-100% 13C; U-100% 15N] AcrA(61-210DD), 50 mM potassium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
31 mM [U-100% 15N] AcrA(61-210DD), 50 mM potassium phosphate, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMAcrA(61-210DD)[U-100% 15N]1
50 mMpotassium phosphate1
1 mMAcrA(61-210DD)[U-100% 13C; U-100% 15N]2
50 mMpotassium phosphate2
1 mMAcrA(61-210DD)[U-100% 15N]3
50 mMpotassium phosphate3
Sample conditionsIonic strength: 50 / pH: 6.4 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE7502
Bruker AvanceBrukerAVANCE6003
Bruker AvanceBrukerAVANCE5004

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Processing

NMR software
NameVersionDeveloperClassification
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
ATNOSCANDIDHerrmann, Guntert, Wuthrichgeometry optimization
SparkyGoddardchemical shift assignment
TopSpin2Bruker Biospinprocessing
RefinementMethod: simulated annealing / 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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