2GRX

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

PDB DOI: https://doi.org/10.2210/pdb2GRX/pdb

Classification: METAL TRANSPORT
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2006-04-25 Released: 2006-06-13
Deposition Author(s): Pawelek, P.D., Allaire, M., Coulton, J.W.

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

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.2 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

PubMed: 16741125 Search on PubMed
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.

Macromolecule Content

Total Structure Weight: 216.87 kDa
Atom Count: 12,533
Modelled Residue Count: 1,549
Deposited Residue Count: 1,908
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferrichrome-iron receptor	A, B	725	Escherichia coli	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06971
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein tonB	C, D	229	Escherichia coli	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02929
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	5		N/A	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G17606RK GlyCosmos: G17606RK

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FCI Query on FCI Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain Y [auth B] MOL2 format, chain O [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain O [auth A] mmCIF format, chain Y [auth B]	O [auth A], Y [auth B]	FERRICROCIN-IRON C₂₈ H₄₄ Fe N₉ O₁₃ FNBCUYMSQPYITB-AFXYHRJJSA-N		Interactions Focus chain O [auth A] Focus chain Y [auth B] Interactions & Density Focus chain O [auth A] Focus chain Y [auth B]
FTT Query on FTT Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	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		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
MYR Query on MYR Download Ideal Coordinates CCD File SDF format, chain W [auth B] MOL2 format, chain W [auth B] mmCIF format, chain W [auth B]	W [auth B]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Focus chain W [auth B] Interactions & Density Focus chain W [auth B]
DAO Query on DAO Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain V [auth B] MOL2 format, chain M [auth A] MOL2 format, chain V [auth B] mmCIF format, chain M [auth A] mmCIF format, chain V [auth B]	M [auth A], V [auth B]	LAURIC ACID C₁₂ H₂₄ O₂ POULHZVOKOAJMA-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain V [auth B] Interactions & Density Focus chain M [auth A] Focus chain V [auth B]
DPO Query on DPO Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain U [auth B] MOL2 format, chain L [auth A] MOL2 format, chain U [auth B] mmCIF format, chain L [auth A] mmCIF format, chain U [auth B]	L [auth A], U [auth B]	DIPHOSPHATE O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-J		Interactions Focus chain L [auth A] Focus chain U [auth B] Interactions & Density Focus chain L [auth A] Focus chain U [auth B]
EAP Query on EAP Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain X [auth B] MOL2 format, chain N [auth A] MOL2 format, chain X [auth B] mmCIF format, chain N [auth A] mmCIF format, chain X [auth B]	N [auth A], X [auth B]	2-AMINO-VINYL-PHOSPHATE C₂ H₆ N O₄ P KYMLMTPYCDIFEC-OWOJBTEDSA-N		Interactions Focus chain N [auth A] Focus chain X [auth B] Interactions & Density Focus chain N [auth A] Focus chain X [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain P [auth B]	G [auth A], P [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain P [auth B]

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 = 234.32	α = 90
b = 91.84	β = 118.86
c = 138.51	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-06-13

Deposition Author(s):

Pawelek, P.D.

Allaire, M.

Coulton, J.W.

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
Version 2.2: 2024-11-13
Changes: Data collection, Structure summary

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2GRX

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2