Download MendeleyCrystal Structure of YedP, phosphatase-like domain protein from Escherichia coli K12
Kim, Y., Joachimiak, A., Cymborowski, M., Skarina, T., Savchenko, A., Edwards, A.To be published.
1XVI | pdb_00001xvi
Crystal Structure of YedP, phosphatase-like domain protein from Escherichia coli K12
- PDB DOI: https://doi.org/10.2210/pdb1XVI/pdb
- Classification: HYDROLASE
- Organism(s): Escherichia coli K-12
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2004-10-28 Released: 2004-12-14
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.26 Å
- R-Value Free: 0.243 (Depositor), 0.240 (DCC)
- R-Value Work: 0.184 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.190 (Depositor)
wwPDB Validation 3D Report Full Report
This is version 1.3 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 mannosyl-3-phosphoglycerate phosphatase | 275 | Escherichia coli K-12 | Mutation(s): 0 Gene Names: yedP EC: 3.1.3.70 |  | |
UniProt | |||||
Find proteins for P76329 (Escherichia coli (strain K12)) Explore P76329 Go to UniProtKB: P76329 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P76329 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 1PE Query on 1PE | E [auth A] | PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N |  | ||
| PG4 Query on PG4 | F [auth A] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N |  | ||
| PGE Query on PGE | G [auth A] | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N |  | ||
| SO4 Query on SO4 | C [auth A], D [auth A], H [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.26 Å
- R-Value Free: 0.243 (Depositor), 0.240 (DCC)
- R-Value Work: 0.184 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.190 (Depositor)
Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 54.783 | α = 90 |
| b = 79.975 | β = 99.56 |
| c = 75.471 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| SBC-Collect | data collection |
| HKL-2000 | data scaling |
| SHARP | phasing |
Entry History
Deposition Data
- Released Date: 2004-12-14 Deposition Author(s): Kim, Y., Joachimiak, A., Cymborowski, M., Skarina, T., Savchenko, A., Edwards, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2004-12-14
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations
