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- PDB-1zdx: Solution Structure of the type 1 pilus assembly platform FimD(25-125) -

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Basic information

Entry
Database: PDB / ID: 1zdx
TitleSolution Structure of the type 1 pilus assembly platform FimD(25-125)
ComponentsOuter membrane usher protein fimD
KeywordsMEMBRANE PROTEIN / BETA SHEET / ALPHA HELIX
Function / homology
Function and homology information


fimbrial usher porin activity / pilus assembly / cell outer membrane
Similarity search - Function
PapC, N-terminal domain / Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain ...PapC, N-terminal domain / Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain / Fimbrial biogenesis outer membrane usher protein signature. / PapC-like, C-terminal domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Outer membrane usher protein FimD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNishiyama, M. / Horst, R. / Herrmann, T. / Vetsch, M. / Bettendorff, P. / Ignatov, O. / Grutter, M. / Wuthrich, K. / Glockshuber, R. / Capitani, G.
CitationJournal: Embo J. / Year: 2005
Title: Structural basis of chaperone-subunit complex recognition by the type 1 pilus assembly platform FimD.
Authors: Nishiyama, M. / Horst, R. / Eidam, O. / Herrmann, T. / Ignatov, O. / Vetsch, M. / Bettendorff, P. / Jelesarov, I. / Glockshuber, R. / Capitani, G.
History
DepositionApr 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: 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
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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane usher protein fimD


Theoretical massNumber of molelcules
Total (without water)10,8661
Polymers10,8661
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #11closest to the average

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Components

#1: Protein Outer membrane usher protein fimD


Mass: 10866.235 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN Residues 70-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimD / Production host: Escherichia coli (E. coli) / References: UniProt: P30130

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: Uniform labeling with 13C, 15N; 90 % H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 293 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 DRXBrukerDRX5001
Bruker DRXBrukerDRX7502
Bruker AVANCEBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
ATHNOS/CANDIDHerrmannstructure solution
ATHNOS/CANDIDHerrmannrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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