Download MendeleyPutative solute-binding protein from Yersinia pestis.
Osipiuk, J., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A.To be published.
3RY3
Putative solute-binding protein from Yersinia pestis.
- PDB DOI: https://doi.org/10.2210/pdb3RY3/pdb
- Classification: TRANSPORT PROTEIN
- Organism(s): Yersinia pestis CO92
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2011-05-10 Released: 2011-05-18
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.43 Å
- R-Value Free: 0.208
- R-Value Work: 0.173
- R-Value Observed: 0.174
wwPDB Validation 3D Report Full Report
This is version 1.5 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 solute-binding protein | 528 | Yersinia pestis CO92 | Mutation(s): 0 Gene Names: oppA4, y1231, YPO2660, YP_2461 |  | |
UniProt | |||||
Find proteins for A0A5P8YI66 (Yersinia pestis) Explore A0A5P8YI66 Go to UniProtKB: A0A5P8YI66 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A5P8YI66 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ACT Query on ACT | C [auth B], D [auth B] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.43 Å
- R-Value Free: 0.208
- R-Value Work: 0.173
- R-Value Observed: 0.174
- Space Group: C 2 2 21
- Diffraction Data: https://doi.org/10.18430/m33ry3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 157.036 | α = 90 |
| b = 171.322 | β = 90 |
| c = 128.842 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| SBC-Collect | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| SHELXD | phasing |
| MLPHARE | phasing |
| DM | phasing |
| SOLVE | phasing |
| RESOLVE | phasing |
| HKL-3000 | phasing |
| PHENIX | refinement |
Entry History
Deposition Data
- Released Date: 2011-05-18 Deposition Author(s): Osipiuk, J., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Revision History (Full details and data files)
- Version 1.0: 2011-05-18
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-11-08
Changes: Refinement description - Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2019-08-14
Changes: Data collection, Refinement description - Version 1.5: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary
