Download MendeleyCrystal structure of Putative glycerophosphoryl diester phosphodiesterase (YP_165505.1) from Silicibacter pomeroyi DSS-3 at 1.60 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3L12
Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (YP_165505.1) from Silicibacter pomeroyi DSS-3 at 1.60 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3L12/pdb
- Classification: HYDROLASE
- Organism(s): Ruegeria pomeroyi
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-12-10 Released: 2009-12-29
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.187
- R-Value Work: 0.156
- R-Value Observed: 0.158
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 Glycerophosphoryl diester phosphodiesterase | 313 | Ruegeria pomeroyi | Mutation(s): 0 Gene Names: SPO0236 |  | |
UniProt | |||||
Find proteins for Q5LX22 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LX22 Go to UniProtKB: Q5LX22 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q5LX22 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CL Query on CL | D [auth A], E [auth A], F [auth A], J [auth B], K [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| MG Query on MG | C [auth A], H [auth B], I [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| UNL Query on UNL | G [auth A], L [auth B] | Unknown ligand JLVVSXFLKOJNIY-UHFFFAOYSA-N | |||
| 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: 1.60 Å
- R-Value Free: 0.187
- R-Value Work: 0.156
- R-Value Observed: 0.158
- Space Group: P 1 21 1
- Diffraction Data: https://doi.org/10.18430/M33L12
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 50.409 | α = 90 |
| b = 136.411 | β = 118 |
| c = 50.548 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SHELX | phasing |
| MolProbity | model building |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| MOSFLM | data reduction |
| SHELXD | phasing |
| autoSHARP | phasing |
Entry History
Deposition Data
- Released Date: 2009-12-29 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-12-29
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-02-01
Changes: Database references, Derived calculations - Version 1.5: 2024-10-09
Changes: Data collection, Refinement description, Structure summary
