Download MendeleyCrystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 2.05 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3KS5
Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 2.05 A resolution
- PDB DOI: 10.2210/pdb3KS5/pdb
- Classification: HYDROLASE
- Organism(s): Agrobacterium fabrum str. C58
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-11-20 Released: 2009-12-08
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.05 Å
- R-Value Free: 0.244
- R-Value Work: 0.212
- R-Value Observed: 0.214
wwPDB Validation 3D Report Full Report
This is version 1.4 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 | A, B | 250 | Agrobacterium fabrum str. C58 | Mutation(s): 0 Gene Names: 17743486, AGR_pAT_81, Atu5061, glpQ |  |
UniProt | |||||
Find proteins for A9CLR1 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CLR1 Go to UniProtKB: A9CLR1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A9CLR1 | ||||
Protein Feature ViewExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EDO Query on EDO | H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | Ligand Interaction | |
| ACT Query on ACT | D [auth A], E [auth A], F [auth A], G [auth A], N [auth B], | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | Ligand Interaction | |
| FE Query on FE | C [auth A], M [auth B] | FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N |  | Ligand Interaction | |
| 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: 2.05 Å
- R-Value Free: 0.244
- R-Value Work: 0.212
- R-Value Observed: 0.214
- Space Group: P 41 21 2
- Diffraction Data DOI: 10.18430/M33KS5
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 84.153 | α = 90 |
| b = 84.153 | β = 90 |
| c = 214.882 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SHARP | phasing |
| MolProbity | model building |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
Entry History
Deposition Data
- Released Date: 2009-12-08 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-12-08
Type: Initial release - Version 1.1: 2011-07-13
Changes: 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
