SAXSdb — 2jbv

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

CHOLINE OXIDASE

ARTHROBACTER GLOBIFORMIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(4aS,10aR)-7,8-dimethyl-2,4-dioxo-1,3,4,4a,5,10a-hexahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate ; × 1 DIMETHYL SULFOXIDE × 1 UNKNOWN ATOM OR ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	;[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(4aS,10aR)-7,8-dimethyl-2,4-dioxo-1,3,4,4a,5,10a-hexahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate ; × 1 DIMETHYL SULFOXIDE × 1 UNKNOWN ATOM OR ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7X2H8_ARTGO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–546； UniProt 1–546 Author chain B； PDBConstruct 1–546； UniProt 1–546

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	2jbv
Deposition date deposition_date	2006-12-13
Structure title title	Crystal structure of choline oxidase reveals insights into the catalytic mechanism
Keywords keywords	;ALCOHOL OXIDATION, FLAVOENYZME OXIDASE, COVALENTLY LINKED FAD, ARTHROBACTER GLOBIFORMIS, C4A-ADDUCT, FLAVOPROTEIN, OXIDOREDUCTASE, GLUCOSE-METHANOL-CHOLINE OXIDOREDUCTASE ENZYME SUPERFAMILY ;; OXIDOREDUCTASE
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.

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2jbv__assembly_1__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
2	1	`2jbv__assembly_2__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	CHOLINE OXIDASE
Molecular weight formula_weight	59898.8 kDa
EC 编号 ec_number	1.1.3.17
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9252

MHIDNIENLSDREFDYIVVGGGSAGAAVAARLSEDPAVSVALVEAGPDDRGVPEVLQLDRWMELLESGYDWDYPIEPQENGNSFMRHARAKVMGGCSSHNSCIAFWAPREDLDEWEAKYGATGWNAEAAWPLYKRLETNEDAGPDAPHHGDSGPVHLMNVPPKDPTGVALLDACEQAGIPRAKFNTGTTVVNGANFFQINRRADGTRSSSSVSYIHPIVEQENFTLLTGLRARQLVFDADRRCTGVDIVDSAFGHTHRLTARNEVVLSTGAIDTPKLLMLSGIGPAAHLAEHGIEVLVDSPGVGEHLQDHPEGVVQFEAKQPMVAESTQWWEIGIFTPTEDGLDRPDLMMHYGSVPFDMNTLRHGYPTTENGFSLTPNVTHARSRGTVRLRSRDFRDKPMVDPRYFTDPEGHDMRVMVAGIRKAREIAAQPAMAEWTGRELSPGVEAQTDEELQDYIRKTHNTVYHPVGTVRMGAVEDEMSPLDPELRVKGVTGLRVADASVMPEHVTVNPNITVMMIGERCADLIRSARAGETTTADAELSAALA

Source Source

Source organism organism	ARTHROBACTER GLOBIFORMIS
NCBI taxonomy ID ncbi_taxonomy_id	1665
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	;[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(4aS,10aR)-7,8-dimethyl-2,4-dioxo-1,3,4,4a,5,10a-hexahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate ;
Molecular weight formula_weight	789.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	UNKNOWN ATOM OR ION
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	969

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2jbvA01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2jbvA02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	450 — Glucose Oxidase; domain 2
Homologous superfamily homologous superfamily	10 — Glucose Oxidase, domain 2

Domain ID domain_id	2jbvA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2jbvA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	410 — Cholesterol Oxidase; domain 2
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	2jbvB01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2jbvB02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	450 — Glucose Oxidase; domain 2
Homologous superfamily homologous superfamily	10 — Glucose Oxidase, domain 2

Domain ID domain_id	2jbvB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2jbvB04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	410 — Cholesterol Oxidase; domain 2
Homologous superfamily homologous superfamily	40 —

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7. Citations (7)

Role of Glu312 in Binding and Positioning of the Substrate for the Hydride Transfer Reaction in Choline Oxidase.

Biochemistry (2008)

PMID: 18072756 · DOI: 10.1021/BI7017943 PRIMARY

Effects of Reversing the Protein Positive Charge in the Proximity of the Flavin N(1) Locus of Choline Oxidase

Biochemistry (2006)

PMID: 16519539 · DOI: 10.1021/BI052514M

On the Catalytic Mechanism of Choline Oxidase

J.Am.Chem.Soc. (2005)

PMID: 15713082 · DOI: 10.1021/JA044541Q

On the Catalytic Role of the Conserved Active Site Residue His466 of Choline Oxidase

Biochemistry (2005)

PMID: 15654745 · DOI: 10.1021/BI048056J

;Cloning, Sequence Analysis, and Purification of Choline Oxidase from Arthrobacter Globiformis: A Bacterial Enzyme Involved in Osmotic Stress Tolerance ;

Arch.Biochem.Biophys. (2004)

PMID: 14678796 · DOI: 10.1016/J.ABB.2003.10.003

The Trimethylammonium Headgroup of Choline is a Major Determinant for Substrate Binding and Specificity in Choline Oxidase

Arch.Biochem.Biophys. (2004)

PMID: 15369826 · DOI: 10.1016/J.ABB.2004.07.011

Kinetic Mechanism of Choline Oxidase from Arthrobacter Globiformis

Biochim.Biophys.Acta (2003)

PMID: 12637017 · DOI: 10.1016/S1570-9639(03)00003-7

Unit-cell length a length_a	84.355 Å
Unit-cell length b length_b	84.355 Å
Unit-cell length c length_c	343.450 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.860 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1710
R_work r_work	0.1690
R_free r_free	0.2120

Crystal structure of choline oxidase reveals insights into the catalytic mechanism

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

CHOLINE 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

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (7)

Crystal structure of choline oxidase reveals insights into the catalytic mechanism

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

CHOLINE 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

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (7)