Download MendeleyCrystal structure of periplasmic glycerophosphodiester phosphodiesterase from Escherichia coli
Malashkevich, V.M., Fedorov, E., Almo, S.C.To be published.
1YDY
Crystal structure of periplasmic glycerophosphodiester phosphodiesterase from Escherichia coli
- PDB DOI: https://doi.org/10.2210/pdb1YDY/pdb
- Classification: HYDROLASE
- Organism(s): Escherichia coli
- Expression System: Escherichia coli BL21
- Mutation(s): No
- Deposited: 2004-12-27 Released: 2005-01-25
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.228
- R-Value Work: 0.187
- R-Value Observed: 0.187
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 |
| Glycerophosphoryl diester phosphodiesterase | 356 | Escherichia coli | Mutation(s): 0 Gene Names: glpQ EC: 3.1.4.46 |  | |
UniProt | |||||
Find proteins for P09394 (Escherichia coli (strain K12)) Explore P09394 Go to UniProtKB: P09394 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P09394 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | D [auth A], F [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| CA Query on CA | C [auth A], E [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.228
- R-Value Work: 0.187
- R-Value Observed: 0.187
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 63.789 | α = 90 |
| b = 74.469 | β = 90 |
| c = 157.219 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| SCALEPACK | data scaling |
| AMoRE | phasing |
Entry History
Deposition Data
- Released Date: 2005-01-25 Deposition Author(s): Malashkevich, V.N., Fedorov, E., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)
Revision History (Full details and data files)
- Version 1.0: 2005-01-25
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.3: 2017-10-11
Changes: Refinement description - Version 1.4: 2021-02-03
Changes: Derived calculations, Structure summary - Version 1.5: 2023-08-23
Changes: Data collection, Database references, Refinement description
