2GRX

Crystal structure of TonB in complex with FhuA, E. coli outer membrane receptor for ferrichrome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.284 
  • R-Value Observed: 0.299 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structure of TonB in complex with FhuA, E. coli outer membrane receptor.

Pawelek, P.D.Croteau, N.Ng-Thow-Hing, C.Khursigara, C.M.Moiseeva, N.Allaire, M.Coulton, J.W.

(2006) Science 312: 1399-1402

  • DOI: https://doi.org/10.1126/science.1128057
  • Primary Citation of Related Structures:  
    2GRX

  • PubMed Abstract: 

    The cytoplasmic membrane protein TonB spans the periplasm of the Gram-negative bacterial cell envelope, contacts cognate outer membrane receptors, and facilitates siderophore transport. The outer membrane receptor FhuA from Escherichia coli mediates TonB-dependent import of ferrichrome. We report the 3.3 angstrom resolution crystal structure of the TonB carboxyl-terminal domain in complex with FhuA. TonB contacts stabilize FhuA's amino-terminal residues, including those of the consensus Ton box sequence that form an interprotein beta sheet with TonB through strand exchange. The highly conserved TonB residue arginine-166 is oriented to form multiple contacts with the FhuA cork, the globular domain enclosed by the beta barrel.


  • Organizational Affiliation

    Department of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, Quebec, H3A 2B4, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferrichrome-iron receptor
A, B
725Escherichia coliMutation(s): 0 
Gene Names: fhuA
Membrane Entity: Yes 
UniProt
Find proteins for P06971 (Escherichia coli (strain K12))
Explore P06971 
Go to UniProtKB:  P06971
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06971
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein tonB
C, D
229Escherichia coliMutation(s): 0 
Gene Names: tonB
Membrane Entity: Yes 
UniProt
Find proteins for P02929 (Escherichia coli (strain K12))
Explore P02929 
Go to UniProtKB:  P02929
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02929
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-[L-glycero-alpha-D-manno-heptopyranose-(1-5)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2,3-dideoxy-alpha-D-glucoyranose-(1-6)-2-amino-2,3-dideoxy-alpha-D-glucoyranose
E, F
5N/A
Glycosylation Resources
GlyTouCan:  G17606RK
GlyCosmos:  G17606RK
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FCI
Query on FCI

Download Ideal Coordinates CCD File 
O [auth A],
Y [auth B]
FERRICROCIN-IRON
C28 H44 Fe N9 O13
FNBCUYMSQPYITB-AFXYHRJJSA-N
FTT
Query on FTT

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H [auth A]
I [auth A]
J [auth A]
K [auth A]
Q [auth B]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B]
3-HYDROXY-TETRADECANOIC ACID
C14 H28 O3
ATRNZOYKSNPPBF-CYBMUJFWSA-N
MYR
Query on MYR

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W [auth B]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
DAO
Query on DAO

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M [auth A],
V [auth B]
LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
DPO
Query on DPO

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L [auth A],
U [auth B]
DIPHOSPHATE
O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-J
EAP
Query on EAP

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N [auth A],
X [auth B]
2-AMINO-VINYL-PHOSPHATE
C2 H6 N O4 P
KYMLMTPYCDIFEC-OWOJBTEDSA-N
PO4
Query on PO4

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G [auth A],
P [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.284 
  • R-Value Observed: 0.299 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 234.32α = 90
b = 91.84β = 118.86
c = 138.51γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary