Download MendeleyCrystal structure of sugar-binding protein YesO in complex with rhamnogalacturonan trisaccharide
Sugiura, H., Oiki, S., Mikami, B., Murata, K., Hashimoto, W.To be published.
5Z6B
Crystal structure of sugar-binding protein YesO in complex with rhamnogalacturonan trisaccharide
- PDB DOI: 10.2210/pdb5Z6B/pdb
- Classification: TRANSPORT PROTEIN
- Organism(s): Bacillus subtilis subsp. subtilis str. 168
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2018-01-22 Released: 2019-01-23
- Funding Organization(s): Fuji Foundation for Protein Research
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.58 Å
- R-Value Free: 0.204
- R-Value Work: 0.179
- R-Value Observed: 0.181
wwPDB Validation 3D Report Full Report
This is version 2.0 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 |
| Putative ABC transporter substrate-binding protein YesO | A | 427 | Bacillus subtilis subsp. subtilis str. 168 | Mutation(s): 0 Gene Names: yesO, BSU06970 |  |
UniProt | |||||
Find proteins for O31518 (Bacillus subtilis (strain 168)) Explore O31518 Go to UniProtKB: O31518 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O31518 | ||||
Protein Feature ViewExpand | |||||
| |||||
Oligosaccharides
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Chain Length | 2D Diagram | Glycosylation | 3D Interactions |
| 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-2)-[beta-D-galactopyranose-(1-4)]alpha-L-rhamnopyranose | B | 3 |  | N/A | Oligosaccharides Interaction |
Glycosylation Resources | |||||
GlyTouCan: G48077ST GlyCosmos: G48077ST | |||||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.58 Å
- R-Value Free: 0.204
- R-Value Work: 0.179
- R-Value Observed: 0.181
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 42.23 | α = 90 |
| b = 78.592 | β = 102.04 |
| c = 54.075 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Deposited Date: 2018-01-22
- Released Date: 2019-01-23 Deposition Author(s): Sugiura, H., Oiki, S., Mikami, B., Murata, K., Hashimoto, W.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Fuji Foundation for Protein Research | Japan | -- |
Revision History (Full details and data files)
- Version 1.0: 2019-01-23
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
