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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Ferrichrome-iron receptorA, B725Escherichia 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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein tonBC, D229Escherichia 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
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucoyranoseE, F 5N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G17606RK
GlyCosmos:  G17606RK
Small Molecules
Ligands 7 Unique
IDChainsName / 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-JWBZYWNVDF
 Ligand Interaction
FTT
Query on FTT

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
MYR
Query on MYR

Download Ideal Coordinates CCD File 
W [auth B]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
DAO
Query on DAO

Download Ideal Coordinates CCD File 
M [auth A],
V [auth B]
LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
 Ligand Interaction
DPO
Query on DPO

Download Ideal Coordinates CCD File 
L [auth A],
U [auth B]
DIPHOSPHATE
O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-J
 Ligand Interaction
EAP
Query on EAP

Download Ideal Coordinates CCD File 
N [auth A],
X [auth B]
2-AMINO-VINYL-PHOSPHATE
C2 H6 N O4 P
KYMLMTPYCDIFEC-OWOJBTEDSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A],
P [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
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

View Full Validation Report



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