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- PDB-2jmr: NMR structure of the E. coli type 1 pilus subunit FimF -

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Basic information

Entry
Database: PDB / ID: 2jmr
TitleNMR structure of the E. coli type 1 pilus subunit FimF
ComponentsfimF
KeywordsCELL ADHESION / Protein
Function / homology
Function and homology information


pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / cell adhesion
Similarity search - Function
Fimbrial-type adhesion domain / Fimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGossert, A.D. / Bettendorff, P. / Puorger, C. / Vetsch, M. / Herrmann, T. / Fiorito, F. / Hiller, S. / Glockshuber, R. / Wuthrich, K.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: NMR structure of the Escherichia coli type 1 pilus subunit FimF and its interactions with other pilus subunits.
Authors: Gossert, A.D. / Bettendorff, P. / Puorger, C. / Vetsch, M. / Herrmann, T. / Glockshuber, R. / Wuthrich, K.
History
DepositionNov 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents ..._pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Advisory / Database references / Other
Category: database_2 / pdbx_database_remark / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _pdbx_database_status.status_code_nmr_data
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Remark 999SEQUENCE The C-terminal extension (residues 156-179) serves as an internal purification tag and ...SEQUENCE The C-terminal extension (residues 156-179) serves as an internal purification tag and self-complementing donor strand, which is essential for the stability of the protein fold.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: fimF


Theoretical massNumber of molelcules
Total (without water)19,1881
Polymers19,1881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein fimF


Mass: 19188.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) star / References: UniProt: P08189

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1214D APSY-HN(CO)CA
1314D APSY-COHNCA
1413D 1H-15N NOESY
1513D 1H-15N TOCSY
1613D 1H-13C NOESY
1712D 1H-15N HSQC
1812D 1H-13C HSQC

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Sample preparation

DetailsContents: 1.4 mM [U-99% 13C; U-99% 15N] FimF, 25 mM sodium phosphate, 100 mM sodium chloride, 0.05 % sodium azide, 5 % D2O, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.4 mMFimF[U-99% 13C; U-99% 15N]1
25 mMsodium phosphate1
100 mMsodium chloride1
0.05 %sodium azide1
5 %D2O1
Sample conditionspH: 6.8 / Temperature: 310.1 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.5.5Rochus, Kellerdata analysis
OPALpLuginbuhl, Guntert, Billeter and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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