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- PDB-2mpv: Structural insight into host recognition and biofilm formation by... -

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Basic information

Entry
Database: PDB / ID: 2mpv
TitleStructural insight into host recognition and biofilm formation by aggregative adherence fimbriae of enteroaggregative Esherichia coli
ComponentsMajor fimbrial subunit of aggregative adherence fimbria II AafA
KeywordsPROTEIN BINDING / AAF / EAEC / Biofilm
Function / homologyImmunoglobulin-like - #2910 / Immunoglobulin-like / Sandwich / Mainly Beta / Major fimbrial subunit of aggregative adherence fimbria II AafA
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / distance geometry, simulated annealing
Model detailslowest energy, model1
AuthorsMatthews, S.J. / Yang, Y. / Berry, A.A. / Pakharukova, N. / Garnett, J.A. / Lee, W. / Cota, E. / Liu, B. / Roy, S. / Tuittila, M. ...Matthews, S.J. / Yang, Y. / Berry, A.A. / Pakharukova, N. / Garnett, J.A. / Lee, W. / Cota, E. / Liu, B. / Roy, S. / Tuittila, M. / Marchant, J. / Inman, K.G. / Ruiz-Perez, F. / Mandomando, I. / Nataro, J.P. / Zavialov, A.V.
CitationJournal: Plos Pathog. / Year: 2014
Title: Structural insight into host recognition by aggregative adherence fimbriae of enteroaggregative Escherichia coli.
Authors: Berry, A.A. / Yang, Y. / Pakharukova, N. / Garnett, J.A. / Lee, W.C. / Cota, E. / Marchant, J. / Roy, S. / Tuittila, M. / Liu, B. / Inman, K.G. / Ruiz-Perez, F. / Mandomando, I. / Nataro, J. ...Authors: Berry, A.A. / Yang, Y. / Pakharukova, N. / Garnett, J.A. / Lee, W.C. / Cota, E. / Marchant, J. / Roy, S. / Tuittila, M. / Liu, B. / Inman, K.G. / Ruiz-Perez, F. / Mandomando, I. / Nataro, J.P. / Zavialov, A.V. / Matthews, S.
History
DepositionJun 4, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major fimbrial subunit of aggregative adherence fimbria II AafA


Theoretical massNumber of molelcules
Total (without water)15,5571
Polymers15,5571
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)1 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Major fimbrial subunit of aggregative adherence fimbria II AafA


Mass: 15556.610 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aafA / Production host: Escherichia coli (E. coli) / References: UniProt: O30595

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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 C(CO)NH
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D HN(CO)CA
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D HNCO
11113D H(CCO)NH

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Sample preparation

DetailsContents: 50 mM sodium acetate, 200 uM [U-100% 13C; U-100% 15N] protein, 50 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium acetate-11
200 uMentity-2[U-100% 13C; U-100% 15N]1
50 mMsodium chloride-31
Sample conditionsIonic strength: 50 / pH: 5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameDeveloperClassification
ARIAJohnson, One Moon Scientificchemical shift assignment
ARIAJohnson, One Moon Scientificstructure solution
ARIALinge, O'Donoghue and Nilgeschemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIArefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 1

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