3nne

Crystal structure of choline oxidase S101A mutant

Method: X-RAY DIFFRACTION

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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	FLAVIN-ADENINE DINUCLEOTIDE × 1 ACETATE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1 ACETATE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1 ACETATE ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1 ACETATE ION × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1 ACETATE ION × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1 ACETATE ION × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1 ACETATE ION × 1 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1 ACETATE ION × 1 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 Author chain C； PDBConstruct 1–546； UniProt 1–546 Author chain D； PDBConstruct 1–546； UniProt 1–546 Author chain E； PDBConstruct 1–546； UniProt 1–546 Author chain F； PDBConstruct 1–546； UniProt 1–546 Author chain G； PDBConstruct 1–546； UniProt 1–546 Author chain H； 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	3nne
Deposition date deposition_date	2010-06-23
Structure title title	Crystal structure of choline oxidase S101A mutant
Keywords keywords	Oxidase, Flavoprotein, Kinetics, Reductive half-reaction, Choline, OXIDOREDUCTASE; 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.

3nne__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3nne__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3nne__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	23.39 Å
Rg (electron density)	22.37 Å
Total Rg	23.19 Å
Atom count	4155
Residues	530
Excluded volume	72563 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3nne__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3nne__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3nne__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3nne__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3nne__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3nne__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3nne__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3nne__assembly_8__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 (4)

Entity 1 Entity 1 polymer

Description description	Choline oxidase
Molecular weight formula_weight	59882.8 kDa
EC 编号 ec_number	1.1.3.17
Mutation mutation	S101A
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	33722

MHIDNIENLSDREFDYIVVGGGSAGAAVAARLSEDPAVSVALVEAGPDDRGVPEVLQLDRWMELLESGYDWDYPIEPQENGNSFMRHARAKVMGGCSSHNACIAFWAPREDLDEWEAKYGATGWNAEAAWPLYKRLETNEDAGPDAPHHGDSGPVHLMNVPPKDPTGVALLDACEQAGIPRAKFNTGTTVVNGANFFQINRRADGTRSSSSVSYIHPIVEQENFTLLTGLRARQLVFDADRRCTGVDIVDSAFGHTHRLTARNEVVLSTGAIDTPKLLMLSGIGPAAHLAEHGIEVLVDSPGVGEHLQDHPEGVVQFEAKQPMVAESTQWWEIGIFTPTEDGLDRPDLMMHYGSVPFDMNTLRHGYPTTENGFSLTPNVTHARSRGTVRLRSRDFRDKPMVDPRYFTDPEGHDMRVMVAGIRKAREIAAQPAMAEWTGRELSPGVEAQTDEELQDYIRKTHNTVYHPVGTVRMGAVEDEMSPLDPELRVKGVTGLRVADASVMPEHVTVNPNITVMMIGERCADLIRSARAGETTTADAELSAALA

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	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	325

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6. Fold Classification (SCOP + CATH) 32 domains

CATH v4.4 (32 domains)

Domain ID domain_id	3nneA01
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	3nneA02
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	3nneA03
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	3nneA04
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	3nneB01
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	3nneB02
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	3nneB03
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	3nneB04
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	3nneC01
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	3nneC02
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	3nneC03
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	3nneC04
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	3nneD01
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	3nneD02
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	3nneD03
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	3nneD04
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	3nneE01
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	3nneE02
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	3nneE03
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	3nneE04
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	3nneF01
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	3nneF02
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	3nneF03
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	3nneF04
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	3nneG01
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	3nneG02
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	3nneG03
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	3nneG04
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	3nneH01
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	3nneH02
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	3nneH03
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	3nneH04
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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Unit-cell length a length_a	69.258 Å
Unit-cell length b length_b	346.029 Å
Unit-cell length c length_c	105.919 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.33 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.470 Å
Low-resolution limit resolution_low	29.990 Å
R factor r_factor	0.2312
R_work r_work	0.2279
R_free r_free	0.2925

Crystal structure of choline oxidase S101A mutant

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

3nne__assembly_4__model_1

3nne__assembly_4__model_1 | I(q)

3nne__assembly_4__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 32 domains

CATH v4.4 (32 domains)

7. Citations (1)

Crystal structure of choline oxidase S101A mutant

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

3nne__assembly_4__model_1

3nne__assembly_4__model_1 | I(q)

3nne__assembly_4__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 32 domains

CATH v4.4 (32 domains)

7. Citations (1)