Download MendeleyThe crystal structure of y333q mutant pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745
Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)To be published.
4RIZ
The crystal structure of Y333Q mutant pyridoxal-dependent decarboxylase from Sphaerobacter thermophilus dsm 20745
- PDB DOI: https://doi.org/10.2210/pdb4RIZ/pdb
- Classification: LYASE
- Organism(s): Sphaerobacter thermophilus DSM 20745
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2014-10-07 Released: 2014-11-12
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.199
- R-Value Work: 0.157
- R-Value Observed: 0.160
This is version 1.2 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 |
| Pyridoxal-dependent decarboxylase | 486 | Sphaerobacter thermophilus DSM 20745 | Mutation(s): 1 Gene Names: Sthe_2364 EC: 4.1.1.15 |  | |
UniProt | |||||
Find proteins for D1C7D8 (Sphaerobacter thermophilus (strain DSM 20745 / S 6022)) Explore D1C7D8 Go to UniProtKB: D1C7D8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D1C7D8 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PMP Query on PMP | E [auth A], K [auth C], L [auth D] | 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C8 H13 N2 O5 P ZMJGSOSNSPKHNH-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | G [auth B], H [auth B], I [auth B], M [auth D] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| NA Query on NA | F [auth A], J [auth B], N [auth D] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| LLP Query on LLP | A, B, C, D | L-PEPTIDE LINKING | C14 H22 N3 O7 P |  | LYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.199
- R-Value Work: 0.157
- R-Value Observed: 0.160
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 69.411 | α = 90 |
| b = 124.659 | β = 99.42 |
| c = 131.849 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-3000 | data collection |
| MLPHARE | phasing |
| PHENIX | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
Entry History
Deposition Data
- Released Date: 2014-11-12 Deposition Author(s): Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2014-11-12
Type: Initial release - Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.2: 2023-12-06
Changes: Data collection
