Download MendeleyCrystal Structure of TolB/Pal complex from Yersinia pestis.
Maltseva, N., Kim, Y., Osipiuk, J., Anderson, W.F., Joachimiak, A.To be published.
4R40
Crystal Structure of TolB/Pal complex from Yersinia pestis.
- PDB DOI: https://doi.org/10.2210/pdb4R40/pdb
- Classification: PROTEIN TRANSPORT
- Organism(s): Yersinia pestis CO92
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2014-08-18 Released: 2014-09-03
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.214
- R-Value Work: 0.170
- R-Value Observed: 0.173
Starting Models: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Protein TolB | 411 | Yersinia pestis CO92 | Mutation(s): 0 Gene Names: tolB, y3055, YPO1124, YP_1032 |  | |
UniProt | |||||
Find proteins for Q8ZGZ1 (Yersinia pestis) Explore Q8ZGZ1 Go to UniProtKB: Q8ZGZ1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8ZGZ1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Peptidoglycan-associated lipoprotein | 141 | Yersinia pestis CO92 | Mutation(s): 0 Gene Names: excC, pal, y3054, YPO1125, YP_1031 |  | |
UniProt | |||||
Find proteins for A0A2U2GZX0 (Yersinia pestis) Explore A0A2U2GZX0 Go to UniProtKB: A0A2U2GZX0 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A2U2GZX0 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | E [auth A], J [auth B], L [auth C], M [auth D] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | H [auth B], I [auth B], K [auth C] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| FMT Query on FMT | F [auth A], G [auth B] | FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, C | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.214
- R-Value Work: 0.170
- R-Value Observed: 0.173
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 47.389 | α = 90 |
| b = 175.252 | β = 89.83 |
| c = 66.268 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SBC-Collect | data collection |
| HKL-3000 | data collection |
| HKL-3000 | phasing |
| MOLREP | phasing |
| PHENIX | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
Entry History
Deposition Data
- Released Date: 2014-09-03 Deposition Author(s): Maltseva, N., Kim, Y., Osipiuk, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Revision History (Full details and data files)
- Version 1.0: 2014-09-03
Type: Initial release - Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.2: 2023-12-06
Changes: Data collection
