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- PDB-5lvy: Structural studies of the Aggregative Adherence Fimbriae of Enter... -

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Basic information

Entry
Database: PDB / ID: 5lvy
TitleStructural studies of the Aggregative Adherence Fimbriae of Enteroaggregative Escherichia coli
ComponentsAdhesin protein
KeywordsCELL ADHESION / Aggregative adherence fimbriae / donor strand complementation / EAEC / E. coli / fibronectin
Function / homologyAdhesin protein
Function and homology information
Biological speciesEscherichia coli O111:H21 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsLiu, B. / Matthews, S.
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Structural and functional studies of Escherichia coli aggregative adherence fimbriae (AAF/V) reveal a deficiency in extracellular matrix binding.
Authors: Jnsson, R. / Liu, B. / Struve, C. / Yang, Y. / Jrgensen, R. / Xu, Y. / Jenssen, H. / Krogfelt, K.A. / Matthews, S.
History
DepositionSep 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 2.0Aug 2, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Structure summary
Category: atom_site / pdbx_nmr_representative ...atom_site / pdbx_nmr_representative / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / struct_conn / struct_sheet_range
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nmr_representative.conformer_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_close_contact.PDB_model_num / _struct_conn.pdbx_dist_value / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adhesin protein


Theoretical massNumber of molelcules
Total (without water)16,4931
Polymers16,4931
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7720 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #1fewest violations

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Components

#1: Protein Adhesin protein


Mass: 16493.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O111:H21 (bacteria) / Gene: aaf5A
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: C9K5V2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic23D HNCO
131isotropic23D HN(CO)CA
141isotropic23D HN(CA)CB
151isotropic23D CBCA(CO)NH
191isotropic23D (H)CCH-TOCSY
181isotropic13D 1H-15N NOESY
171isotropic13D 1H-13C NOESY
161isotropic23D HBHA(CO)NH
1101isotropic23D H(CCO)NH
1111isotropic23D H(CCO)NH

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Sample preparation

DetailsType: solution
Contents: 50 mM U sodium acetate, 50 nM U sodium chloride, 90% H2O/10% D2O
Label: 13C15N / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium acetateU1
50 nMsodium chlorideU1
Sample conditionsIonic strength: 100 mM / Label: 1 / pH: 5.0 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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