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- PDB-3zpd: Solution structure of the FimH adhesin carbohydrate-binding domain -

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Basic information

Entry
Database: PDB / ID: 3zpd
TitleSolution structure of the FimH adhesin carbohydrate-binding domain
ComponentsFIMH
KeywordsCELL ADHESION / BACTERIAL ADHESIN / URINARY TRACT INFECTION / CARBOHYDRATE
Function / homology
Function and homology information


pilus / cell adhesion
Similarity search - Function
FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesESCHERICHIA COLI (E. coli)
MethodSOLUTION NMR / RECOORD
Authorsvan Nuland, N.A.J. / Vanwetswinkel, S. / Vranken, W.F. / Buts, L.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Study of the Structural and Dynamic Effects in the Fimh Adhesin Upon Alpha-D-Heptyl Mannose Binding.
Authors: Vanwetswinkel, S. / Volkov, A.N. / Sterckx, Y.G.J. / Garcia-Pino, A. / Buts, L. / Vranken, W.F. / Bouckaert, J. / Roy, R. / Wyns, L. / Van Nuland, N.A.J.
History
DepositionFeb 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 2.0Jun 14, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FIMH


Theoretical massNumber of molelcules
Total (without water)16,9171
Polymers16,9171
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50LOWEST OVERALL ENERGY
Representative

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Components

#1: Protein FIMH


Mass: 16916.828 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE-BINDING DOMAIN, RESIDUES 10-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: J96 / Plasmid: PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: A2IC68

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: NONE

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Sample preparation

DetailsContents: 93% H2O/7% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.0 1.0 atm298.0 K
26.0 1.0 atm298.0 K
36.0 1.0 atm298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Direct DriveVarianDirect Drive6001
Varian Direct DriveVarianDirect Drive8002
Bruker AVANCEBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
CcpNmr Analysis2.1structure solution
CINGANYstructure solution
NMRPipeANYstructure solution
CYANA1structure solution
DANGLE1.1structure solution
TALOS+ANYstructure solution
CcpNmr AnalysisANYstructure solution
NMRDrawANYstructure solution
RefinementMethod: RECOORD / Software ordinal: 1 / Details: RECOORD PROTOCOL
NMR ensembleConformer selection criteria: LOWEST OVERALL ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 25

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