SAXSdb — 1pj5

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

N,N-dimethylglycine oxidase

Arthrobacter globiformis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SODIUM ION × 4 ACETATE ION × 4 FLAVIN-ADENINE DINUCLEOTIDE × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9AGP8_ARTGO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–830； UniProt 1–830

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	1pj5
Deposition date deposition_date	2003-06-01
Structure title title	Crystal structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with acetate
Keywords keywords	Channelling, FAD binding, folate binding, amine oxidase, 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.

1pj5__assembly_1__model_1

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

Download this curve (.dat)

1pj5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1pj5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	47.08 Å
Rg (electron density)	46.17 Å
Total Rg	46.55 Å
Atom count	25428
Residues	3308
Excluded volume	450330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1pj5__assembly_1__model_1`	tetrameric （4）	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 (5)

Entity 1 Entity 1 polymer

Description description	N,N-dimethylglycine oxidase
Molecular weight formula_weight	90075.5 kDa
EC 编号 ec_number	1.5.3.10
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	8097

MASTPRIVIIGAGIVGTNLADELVTRGWNNITVLDQGPLNMPGGSTSHAPGLVFQTNPSKTMASFAKYTVEKLLSLTEDGVSCFNQVGGLEVATTETRLADLKRKLGYAAAWGIEGRLLSPAECQELYPLLDGENILGGLHVPSDGLASAARAVQLLIKRTESAGVTYRGSTTVTGIEQSGGRVTGVQTADGVIPADIVVSCAGFWGAKIGAMIGMAVPLLPLAHQYVKTTPVPAQQGRNDQPNGARLPILRHQDQDLYYREHGDRYGIGSYAHRPMPVDVDTLGAYAPETVSEHHMPSRLDFTLEDFLPAWEATKQLLPALADSEIEDGFNGIFSFTPDGGPLLGESKELDGFYVAEAVWVTHSAGVAKAMAELLTTGRSETDLGECDITRFEDVQLTPEYVSETSQQNFVEIYDVLHPLQPRLSPRNLRVSPFHARHKELGAFFLEAGGWERPYWFEANAALLKEMPAEWLPPARDAWSGMFSSPIAAAEAWKTRTAVAMYDMTPLKRLEVSGPGALKLLQELTTADLAKKPGAVTYTLLLDHAGGVRSDITVARLSEDTFQLGANGNIDTAYFERAARHQTQSGSATDWVQVRDTTGGTCCIGLWGPLARDLVSKVSDDDFTNDGLKYFRAKNVVIGGIPVTAMRLSYVGELGWELYTSADNGQRLWDALWQAGQPFGVIAAGRAAFSSLRLEKGYRSWGTDMTTEHDPFEAGLGFAVKMAKESFIGKGALEGRTEEASARRLRCLTIDDGRSIVLGKEPVFYKEQAVGYVTSAAYGYTVAKPIAYSYLPGTVSVGDSVDIEYFGRRITATVTEDPLYDPKMTRLRG

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	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

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	1

Entity 4 Entity 4 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1740

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1pj5a1
Class class	b — All beta proteins
Fold Fold fold	b.44 — Elongation factor/aminomethyltransferase common domain
Superfamily Superfamily superfamily	b.44.2 — Aminomethyltransferase beta-barrel domain
Family Family family	b.44.2.1 — Aminomethyltransferase beta-barrel domain

Domain ID domain_id	d1pj5a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

Domain ID domain_id	d1pj5a3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
Family Family family	d.16.1.5 — L-aminoacid/polyamine oxidase

Domain ID domain_id	d1pj5a4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.250 — Folate-binding domain
Superfamily Superfamily superfamily	d.250.1 — Folate-binding domain
Family Family family	d.250.1.1 — Aminomethyltransferase folate-binding domain

CATH v4.4 (5 domains)

Domain ID domain_id	1pj5A01
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	1pj5A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	9 — D-Amino Acid Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — D-Amino Acid Oxidase, subunit A, domain 2

Domain ID domain_id	1pj5A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	120 — Probable tRNA modification gtpase trme; domain 1

Domain ID domain_id	1pj5A04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1400 — Aminomethyltransferase beta-barrel domains

Domain ID domain_id	1pj5A05
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	110 — Aminomethyltransferase beta-barrel domains

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Unit-cell length a length_a	71.381 Å
Unit-cell length b length_b	226.680 Å
Unit-cell length c length_c	120.661 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	8

Space group space_group	C 2 2 2
Space-group number int_tables_number	21
Crystal system crystal_system	—

Resolution resolution	1.610 Å
Low-resolution limit resolution_low	14.990 Å
R factor r_factor	0.1619
R_work r_work	0.1600
R_free r_free	0.1983

Crystal structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with acetate

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

N,N-dimethylglycine 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

1pj5__assembly_1__model_1

1pj5__assembly_1__model_1 | I(q)

1pj5__assembly_1__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 (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) 9 domains

SCOP 2.08 (4 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Crystal structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with acetate

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

N,N-dimethylglycine 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

1pj5__assembly_1__model_1

1pj5__assembly_1__model_1 | I(q)

1pj5__assembly_1__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 (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) 9 domains

SCOP 2.08 (4 domains)

CATH v4.4 (5 domains)

7. Citations (1)