6CR0 | pdb_00006cr0

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 
• Deposition Author(s): Deay III, D., Lovell, S., Battaile, K.P., Petillo, P., Richter, M.
• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.185 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.149 (Depositor) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Improving 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

• DOI: https://doi.org/10.1016/j.abb.2022.109122

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.34 kDa 
• Atom Count: 3,691 
• Modeled Residue Count: 430 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(S)-6-hydroxynicotine oxidase	A	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	H [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
MPD	D [auth A], E [auth A], F [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACT	G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
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 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.149 (Depositor) 
• R-Value Observed: 0.150 (Depositor) 

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 Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
CRANK2	phasing

Structure Validation

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.

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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  

• 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