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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.185 (Depositor), 0.190 (DCC)
R-Value Work:
0.149 (Depositor), 0.160 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A075BSX9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.185 (Depositor), 0.190 (DCC)
R-Value Work: 0.149 (Depositor), 0.160 (DCC)
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-03-28

Deposition Author(s):

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