Download MendeleyGeneralized enzymatic mechanism of catalysis by tetrameric L-asparaginases from mesophilic bacteria.
Strzelczyk, P., Zhang, D., Dyba, M., Wlodawer, A., Lubkowski, J.(2020) Sci Rep 10: 17516
6WZ4
Complex of mutant (K173M) of Pseudomonas 7A Glutaminase-Asparaginase with L-Asp at pH 6. Covalent acyl-enzyme intermediate
- PDB DOI: https://doi.org/10.2210/pdb6WZ4/pdb
- Classification: HYDROLASE
- Organism(s): Pseudomonas putida KT2440
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2020-05-13 Released: 2020-10-14
- Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.58 Å
- R-Value Free: 0.157
- R-Value Work: 0.139
- R-Value Observed: 0.139
Starting Model: experimental
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This is version 1.3 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Glutaminase-asparaginase | 337 | Pseudomonas putida KT2440 | Mutation(s): 1 Gene Names: ansB, PP_2453 EC: 3.5.1.38 |  | |
UniProt | |||||
Find proteins for Q88K39 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88K39 Go to UniProtKB: Q88K39 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q88K39 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ASP (Subject of Investigation/LOI) Query on ASP | E [auth A], F [auth B], G [auth C], H [auth D] | ASPARTIC ACID C4 H7 N O4 CKLJMWTZIZZHCS-REOHCLBHSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.58 Å
- R-Value Free: 0.157
- R-Value Work: 0.139
- R-Value Observed: 0.139
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 78.034 | α = 90 |
| b = 129.754 | β = 118.72 |
| c = 81.409 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-3000 | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-10-14 Deposition Author(s): Strzelczyk, P., Zhang, D., Wlodawer, A., Lubkowski, J.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Cancer Institute (NIH/NCI) | United States | -- |
Revision History (Full details and data files)
- Version 1.0: 2020-10-14
Type: Initial release - Version 1.1: 2020-10-21
Changes: Database references - Version 1.2: 2023-10-18
Changes: Data collection, Database references, Refinement description - Version 1.3: 2024-10-09
Changes: Structure summary
