2bvg

Crystal structure of 6-hydoxy-D-nicotine oxidase from Arthrobacter nicotinovorans. Crystal Form 1 (P21)

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

6-HYDROXY-D-NICOTINE OXIDASE

ARTHROBACTER NICOTINOVORANS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8GAG1_ARTNI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–459； UniProt 1–459 Author chain B； PDBConstruct 1–459； UniProt 1–459 Author chain C； PDBConstruct 1–459； UniProt 1–459 Author chain D； PDBConstruct 1–459； UniProt 1–459

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2bvg
Deposition date deposition_date	2005-06-28
Structure title title	Crystal structure of 6-hydoxy-D-nicotine oxidase from Arthrobacter nicotinovorans. Crystal Form 1 (P21)
Keywords keywords	AUTOFLAVINYLATION, ENANTIOMERIC SUBSTRATES, FLAVOENZYMES, NICOTINE DEGRADATION, OXIDASE; OXIDASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2bvg__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2bvg__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2bvg__assembly_3__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	22.80 Å
Rg (electron density)	21.91 Å
Total Rg	22.79 Å
Atom count	3452
Residues	453
Excluded volume	60898 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2bvg__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2bvg__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2bvg__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2bvg__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	6-HYDROXY-D-NICOTINE OXIDASE
Molecular weight formula_weight	48918.1 kDa
EC 编号 ec_number	1.5.3.6
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	13808

MVSSKLATPLSIQGEVIYPDDSGFDAIANIWDGRHLQRPSLIARCLSAGDVAKSVRYACDNGLEISVRSGGHNPNGYATNDGGIVLDLRLMNSIHIDTAGSRARIGGGVISGDLVKEAAKFGLAAVTGMHPKVGFCGLALNGGVGFLTPKYGLASDNILGATLVTATGDVIYCSDDERPELFWAVRGAGPNFGVVTEVEVQLYELPRKMLAGFITWAPSVSELAGLLTSLLDALNEMADHIYPSVFVGVDENRAPSVTVCVGHLGGLDIAERDIARLRGLGRTVSDSIAVRSYDEVVALNAEVGSFEDGMSNLWIDREIAMPNARFAEAIAGNLDKFVSEPASGGSVKLEIEGMPFGNPKRTPARHRDAMGVLALAEWSGAAPGSEKYPELARELDAALLRAGVTTSGFGLLNNNSEVTAEMVAEVYKPEVYSRLAAVKREYDPENRFRHNYNIDPEGS

Source Source

Source organism organism	ARTHROBACTER NICOTINOVORANS
NCBI taxonomy ID ncbi_taxonomy_id	29320
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2bvga1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.145 — FAD-binding/transporter-associated domain-like
Superfamily Superfamily superfamily	d.145.1 — FAD-binding/transporter-associated domain-like
Family Family family	d.145.1.1 — FAD-linked oxidases, N-terminal domain

Domain ID domain_id	d2bvga2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.32 — FAD-linked oxidases, C-terminal domain
Family Family family	d.58.32.5 — 6-hydroxy-d-nicotine oxidase

Domain ID domain_id	d2bvgb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.145 — FAD-binding/transporter-associated domain-like
Superfamily Superfamily superfamily	d.145.1 — FAD-binding/transporter-associated domain-like
Family Family family	d.145.1.1 — FAD-linked oxidases, N-terminal domain

Domain ID domain_id	d2bvgb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.32 — FAD-linked oxidases, C-terminal domain
Family Family family	d.58.32.5 — 6-hydroxy-d-nicotine oxidase

Domain ID domain_id	d2bvgc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.145 — FAD-binding/transporter-associated domain-like
Superfamily Superfamily superfamily	d.145.1 — FAD-binding/transporter-associated domain-like
Family Family family	d.145.1.1 — FAD-linked oxidases, N-terminal domain

Domain ID domain_id	d2bvgc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.32 — FAD-linked oxidases, C-terminal domain
Family Family family	d.58.32.5 — 6-hydroxy-d-nicotine oxidase

Domain ID domain_id	d2bvgd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.145 — FAD-binding/transporter-associated domain-like
Superfamily Superfamily superfamily	d.145.1 — FAD-binding/transporter-associated domain-like
Family Family family	d.145.1.1 — FAD-linked oxidases, N-terminal domain

Domain ID domain_id	d2bvgd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.32 — FAD-linked oxidases, C-terminal domain
Family Family family	d.58.32.5 — 6-hydroxy-d-nicotine oxidase

CATH v4.4 (12 domains)

Domain ID domain_id	2bvgA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2

Domain ID domain_id	2bvgA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2bvgA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2bvgB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2

Domain ID domain_id	2bvgB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2bvgB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2bvgC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2

Domain ID domain_id	2bvgC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2bvgC03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2bvgD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2

Domain ID domain_id	2bvgD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2bvgD03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	103.640 Å
Unit-cell length b length_b	95.230 Å
Unit-cell length c length_c	122.980 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.06 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.180 Å
Low-resolution limit resolution_low	43.490 Å
R factor r_factor	0.2530
R_work r_work	0.2530
R_free r_free	0.2890

Crystal structure of 6-hydoxy-D-nicotine oxidase from Arthrobacter nicotinovorans. Crystal Form 1 (P21)

1. Protein Identity and Related Structures Protein Identity & Related Structures

6-HYDROXY-D-NICOTINE OXIDASE

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2bvg__assembly_3__model_1

2bvg__assembly_3__model_1 | I(q)

2bvg__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of 6-hydoxy-D-nicotine oxidase from Arthrobacter nicotinovorans. Crystal Form 1 (P21)

1. Protein Identity and Related Structures Protein Identity & Related Structures

6-HYDROXY-D-NICOTINE OXIDASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2bvg__assembly_3__model_1

2bvg__assembly_3__model_1 | I(q)

2bvg__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)