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- PDB-1zwt: Structure of the globular head domain of the bundlin, BfpA, of th... -

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Basic information

Entry
Database: PDB / ID: 1zwt
TitleStructure of the globular head domain of the bundlin, BfpA, of the bundle-forming pilus of Enteropathogenic E.coli
ComponentsMajor structural subunit of bundle-forming pilus
KeywordsCELL ADHESION / alpha-beta fold / beta-sandwich / one disulfide bond
Function / homology
Function and homology information


Major structural subunit of bundle-forming pilus / Bundlin / TcpA-like pilin / TcpA-like pilin / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation site / Pilin-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Major structural subunit of bundle-forming pilus
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / Simulated annealing with NMR restraints using ARIA
AuthorsRamboarina, S. / Fernandes, P.J. / Daniell, S. / Islam, S. / Frankel, G. / Booy, F. / Donnenberg, M.S. / Matthews, S.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Structure of the Bundle-forming Pilus from Enteropathogenic Escherichia coli
Authors: Ramboarina, S. / Fernandes, P.J. / Daniell, S. / Islam, S. / Simpson, P. / Frankel, G. / Booy, F. / Donnenberg, M.S. / Matthews, S.
#1: Journal: J.BIOMOL.NMR / Year: 2004
Title: Complete resonance assignments of bundlin (BfpA) from the bundle-forming pilus of enteropathogenic Escherichia coli
Authors: Ramboarina, S. / Fernandes, P. / Simpson, P. / Frankel, G. / Donnenberg, M. / Matthews, S.
History
DepositionJun 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 structural subunit of bundle-forming pilus


Theoretical massNumber of molelcules
Total (without water)16,4861
Polymers16,4861
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)12 / 100structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #12least number of violations, lowest energy

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Components

#1: Protein Major structural subunit of bundle-forming pilus / Bundle- forming pilin / Bundlin / BFP


Mass: 16486.092 Da / Num. of mol.: 1 / Fragment: BfpA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O127:H6 / Gene: bfpA / Plasmid: pET39b+ / Production host: Escherichia coli (E. coli) / Strain (production host): RY3080 / References: UniProt: P33553
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1313D HBHA(CBCACO)NH
1413D (H)CCH-TOCSY
1513D (H)CC(CO)NH-TOCSY
NMR detailsText: Hydrogen-exchange experiments

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Sample preparation

DetailsContents: 0.5 mM BfpA U-15N,13C, 20 mM sodium phosphate buffer pH 5.2, 90%H20, 10% D2O
Solvent system: 90%H20, 10% D2O
Sample conditionsIonic strength: no salt / pH: 5.2 / Pressure: normal / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grezsiek, Baxprocessing
NMRView5.0.4Johnson and Blevinsdata analysis
ARIA1.2Linge and Nilgesrefinement
RefinementMethod: Simulated annealing with NMR restraints using ARIA / Software ordinal: 1
Details: 577 Ambiguous and 2277 unambiguous NOE restraints, 86 TALOS constraints and 38 hydrogen bonds were imposed during ARIA structure calculations.
NMR representativeSelection criteria: least number of violations, lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 12

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