Download MendeleyImproving the kinetic parameters of nicotine oxidizing enzymes by homologous structure comparison and rational design
Deay, D.O., Seibold, S., Battaile, K.P., Lovell, S., Richter, M.L., Petillo, P.A.(2022) Arch Biochem Biophys : 109122
6CR0
1.55 A resolution structure of (S)-6-hydroxynicotine oxidase from Shinella HZN7
- PDB DOI: https://doi.org/10.2210/pdb6CR0/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Shinella sp. HZN7
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2018-03-16 Released: 2018-03-28
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.55 Å
- R-Value Free: 0.185
- R-Value Work: 0.149
- R-Value Observed: 0.150
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 |
| (S)-6-hydroxynicotine oxidase | 440 | Shinella sp. HZN7 | Mutation(s): 0 Gene Names: nctB, shn_30305 EC: 1.5.3.5 |  | |
UniProt | |||||
Find proteins for A0A075BSX9 (Shinella sp. (strain HZN7)) Explore A0A075BSX9 Go to UniProtKB: A0A075BSX9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A075BSX9 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| FAD Query on FAD | H [auth A] | FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N |  | ||
| MPD Query on MPD | D [auth A], E [auth A], F [auth A] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| ACT Query on ACT | G [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| CA Query on CA | B [auth A], C [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.55 Å
- R-Value Free: 0.185
- R-Value Work: 0.149
- R-Value Observed: 0.150
- Space Group: P 31 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 96.282 | α = 90 |
| b = 96.282 | β = 90 |
| c = 78.628 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PDB_EXTRACT | data extraction |
| CRANK2 | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-03-28 Deposition Author(s): Deay III, D., Lovell, S., Battaile, K.P., Petillo, P., Richter, M.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | P30GM110761 |
| National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA) | United States | 2R44DA033701 |
Revision History (Full details and data files)
- Version 1.0: 2018-03-28
Type: Initial release - Version 1.1: 2019-02-20
Changes: Author supporting evidence, Data collection - Version 1.2: 2019-12-11
Changes: Author supporting evidence - Version 1.3: 2022-01-26
Changes: Database references, Derived calculations - Version 1.4: 2024-04-03
Changes: Data collection, Refinement description
