Download MendeleyStructural Insights into the Catalytic Mechanism of Arabidopsis thaliana Agmatine Deiminase
Burgie, E.S., Bingman, C.A., Phillips Jr., G.N.To be published.
3H7C
Crystal Structure of Arabidopsis thaliana Agmatine Deiminase from Cell Free Expression
- PDB DOI: https://doi.org/10.2210/pdb3H7C/pdb
- Classification: HYDROLASE
- Organism(s): Arabidopsis thaliana
- Mutation(s): No
- Deposited: 2009-04-24 Released: 2009-05-26
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 Å
- R-Value Free: 0.174
- R-Value Work: 0.146
- R-Value Observed: 0.147
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 |
| Agmatine deiminase | A [auth X] | 383 | Arabidopsis thaliana | Mutation(s): 0 Gene Names: AIH, At5g08170, EMB1873, T22D6.110 EC: 3.5.3.12 |  |
UniProt | |||||
Find proteins for Q8GWW7 (Arabidopsis thaliana) Explore Q8GWW7 Go to UniProtKB: Q8GWW7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8GWW7 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 6 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 1PE Query on 1PE | I [auth X] | PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N |  | ||
| 211 Query on 211 | H [auth X] | 2,2',2''-NITRILOTRIETHANOL C6 H15 N O3 GSEJCLTVZPLZKY-UHFFFAOYSA-N |  | ||
| K Query on K | G [auth X] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N |  | ||
| CL Query on CL | B [auth X], C [auth X] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| MG Query on MG | D [auth X] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| NA Query on NA | E [auth X], F [auth X] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A [auth X] | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 Å
- R-Value Free: 0.174
- R-Value Work: 0.146
- R-Value Observed: 0.147
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 123.715 | α = 90 |
| b = 69.932 | β = 98.4 |
| c = 50.917 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| RESOLVE | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| AutoSol | phasing |
Entry History
Deposition Data
- Released Date: 2009-05-26 Deposition Author(s): Burgie, E.S., Bingman, C.A., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)
Revision History (Full details and data files)
- Version 1.0: 2009-05-26
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: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary
