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 10: 3548-3555
6P08
Ternary structure of the E52D mutant of ANT-4'' with Neomycin, AMP and Pyrophosphate
- PDB DOI: https://doi.org/10.2210/pdb6P08/pdb
- Classification: TRANSFERASE/ANTIBIOTIC
- Organism(s): Bacillus sp. (in: firmicutes)
- Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
- Mutation(s): Yes
- Deposited: 2019-05-16 Released: 2020-01-29
- Funding Organization(s): National Science Foundation (NSF, United States), Department of Energy (DOE, United States)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.27 Å
- R-Value Free: 0.225
- R-Value Work: 0.194
- R-Value Observed: 0.196
wwPDB Validation 3D Report Full Report
Currently 6P08 does not have a validation slider image.
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 |
| Kanamycin nucleotidyltransferase | A, B [auth D] | 256 | Bacillus sp. (in: firmicutes) | Mutation(s): 1 Gene Names: knt, kan EC: 2.7.7 |  |
UniProt | |||||
Find proteins for P05058 (Bacillus sp) Explore P05058 Go to UniProtKB: P05058 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P05058 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NMY (Subject of Investigation/LOI) Query on NMY | C [auth A], I [auth A] | NEOMYCIN C23 H46 N6 O13 PGBHMTALBVVCIT-VCIWKGPPSA-N |  | ||
| AMP (Subject of Investigation/LOI) Query on AMP | G [auth A], H [auth A] | ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N |  | ||
| PPV (Subject of Investigation/LOI) Query on PPV | D [auth A], K [auth D] | PYROPHOSPHATE H4 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-N |  | ||
| MG (Subject of Investigation/LOI) Query on MG | E [auth A], F [auth A], J [auth A], L [auth D] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.27 Å
- R-Value Free: 0.225
- R-Value Work: 0.194
- R-Value Observed: 0.196
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 59.75 | α = 90 |
| b = 99.3 | β = 90 |
| c = 101.49 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| iMOSFLM | data reduction |
| Aimless | data scaling |
| PHENIX | phasing |
Structure Validation
Currently 6P08 does not have a validation slider image.
Entry History & Funding Information
Deposition Data
- Released Date: 2020-01-29 Deposition Author(s): Selvaraj, B., Cuneo, M.J.
| 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: 2020-01-29
Type: Initial release - Version 1.1: 2020-05-06
Changes: Database references - Version 1.2: 2020-05-20
Changes: Database references - Version 1.3: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description
