Download Mendeley'Catch and Release": a Variation of the Archetypal Nucleotidyl Transfer Reaction
Selvaraj, B., Kocaman, S., Trifas, M., Serpersu, E.H., Cuneo, M.J.(2020) ACS Catal
6NMK
Binary complex structure of the T130K mutant of ANT-4'' with Neomycin
- PDB DOI: https://doi.org/10.2210/pdb6NMK/pdb
- Classification: transferase/ANTIBIOTIC
- Organism(s): Geobacillus stearothermophilus
- Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
- Mutation(s): No
- Deposited: 2019-01-11 Released: 2020-01-15
- Funding Organization(s): National Science Foundation (NSF, United States), Department of Energy (DOE, United States)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.94 Å
- R-Value Free: 0.210
- R-Value Work: 0.170
- R-Value Observed: 0.172
This is version 1.4 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 |
| Kanamycin nucleotidyltransferase | 256 | Geobacillus stearothermophilus | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for Q57514 (Geobacillus stearothermophilus) Explore Q57514 Go to UniProtKB: Q57514 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q57514 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NMY Query on NMY | C [auth A], G [auth B] | NEOMYCIN C23 H46 N6 O13 PGBHMTALBVVCIT-VCIWKGPPSA-N |  | ||
| CA Query on CA | E [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| MG Query on MG | D [auth A], F [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.94 Å
- R-Value Free: 0.210
- R-Value Work: 0.170
- R-Value Observed: 0.172
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 59 | α = 90 |
| b = 97.71 | β = 90 |
| c = 101.97 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-3000 | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-01-15 Deposition Author(s): Cuneo, M.J., Selvaraj, B.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Science Foundation (NSF, United States) | United States | -- |
| Department of Energy (DOE, United States) | United States | -- |
Revision History (Full details and data files)
- Version 1.0: 2020-01-15
Type: Initial release - Version 1.1: 2020-01-29
Changes: Database references - Version 1.2: 2020-02-26
Changes: Database references - Version 1.3: 2020-05-06
Changes: Database references - Version 1.4: 2024-03-13
Changes: Data collection, Database references, Derived calculations
