Download MendeleyBinding competition between substrates and cryoprotectants in protein crystals directly observed by a hybrid method of in-gel crystallization and high-pressure cryo-cooling in X-ray crystallography
Higashiura, A., Sugiyama, S.To be published.
8Y28
X-ray crystal structure of ALiS5-Streptavidine complex with 20% glycerol using a high-pressure cryocooling method
- PDB DOI: https://doi.org/10.2210/pdb8Y28/pdb
- Classification: CYTOSOLIC PROTEIN
- Organism(s): Streptomyces avidinii
- Mutation(s): No
- Deposited: 2024-01-25 Released: 2025-01-29
- Funding Organization(s): Other private
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.33 ?
- R-Value Free: 0.185 (Depositor), 0.185 (DCC)
- R-Value Work: 0.148 (Depositor), 0.147 (DCC)
- R-Value Observed: 0.150 (Depositor)
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 1.0 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 |
| Streptavidin | 121 | Streptomyces avidinii | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for P22629 (Streptomyces avidinii) Explore P22629 Go to UniProtKB: P22629 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P22629 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | E [auth A], G [auth B], H [auth C], J [auth D] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| DMS Query on DMS | F [auth A], I [auth C] | DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.33 ?
- R-Value Free: 0.185 (Depositor), 0.185 (DCC)
- R-Value Work: 0.148 (Depositor), 0.147 (DCC)
- R-Value Observed: 0.150 (Depositor)
Space Group: P 1 21 1
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 46.666 | ¦Á = 90 |
| b = 85.553 | ¦Â = 98.87 |
| c = 58.343 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-01-29 Deposition Author(s): Higashiura, A., Yamamoto, A., Sugiyama, S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Other private | Japan | -- |
Revision History (Full details and data files)
- Version 1.0: 2025-01-29
Type: Initial release
