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 
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 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Ferrichrome-iron receptor | 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 AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Protein tonB | 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 AnnotationsExpand | |||||
|
Oligosaccharides
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 | ||
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 | O [auth A], Y [auth B] | FERRICROCIN-IRON C28 H44 Fe N9 O13 FNBCUYMSQPYITB-AFXYHRJJSA-N | |||
FTT Query on FTT | H [auth A] I [auth A] J [auth A] K [auth A] Q [auth B] | 3-HYDROXY-TETRADECANOIC ACID C14 H28 O3 ATRNZOYKSNPPBF-CYBMUJFWSA-N | |||
MYR Query on MYR | W [auth B] | MYRISTIC ACID C14 H28 O2 TUNFSRHWOTWDNC-UHFFFAOYSA-N | |||
DAO Query on DAO | M [auth A], V [auth B] | LAURIC ACID C12 H24 O2 POULHZVOKOAJMA-UHFFFAOYSA-N | |||
DPO Query on DPO | L [auth A], U [auth B] | DIPHOSPHATE O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-J | |||
EAP Query on EAP | N [auth A], X [auth B] | 2-AMINO-VINYL-PHOSPHATE C2 H6 N O4 P KYMLMTPYCDIFEC-OWOJBTEDSA-N | |||
PO4 Query on PO4 | 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 = 234.32 | α = 90 |
b = 91.84 | β = 118.86 |
c = 138.51 | γ = 90 |
Software Name | Purpose |
---|---|
CNS | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
HKL-2000 | data scaling |
PHASER | phasing |
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