SAXSdb — 3gsi

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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	(6S)-5,6,7,8-TETRAHYDROFOLATE × 4 MAGNESIUM 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 1–827； UniProt 4–830

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	3gsi
Deposition date deposition_date	2009-03-27
Structure title title	Crystal structure of D552A dimethylglycine oxidase mutant of Arthrobacter globiformis in complex with tetrahydrofolate
Keywords keywords	Oxidoreductase, Channelling, FAD binding, folinic acid, folate binding, amine oxidation; 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.

3gsi__assembly_1__model_1

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

Download this curve (.dat)

3gsi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gsi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.78 Å
Rg (electron density)	45.92 Å
Total Rg	46.30 Å
Atom count	25424
Residues	3308
Excluded volume	450110 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gsi__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	89742.1 kDa
EC 编号 ec_number	1.5.3.10
Mutation mutation	D552A
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	7436

TPRIVIIGAGIVGTNLADELVTRGWNNITVLDQGPLNMPGGSTSHAPGLVFQTNPSKTMASFAKYTVEKLLSLTEDGVSCFNQVGGLEVATTETRLADLKRKLGYAAAWGIEGRLLSPAECQELYPLLDGENILGGLHVPSDGLASAARAVQLLIKRTESAGVTYRGSTTVTGIEQSGGRVTGVQTADGVIPADIVVSCAGFWGAKIGAMIGMAVPLLPLAHQYVKTTPVPAQQGRNDQPNGARLPILRHQDQDLYYREHGDRYGIGSYAHRPMPVDVDTLGAYAPETVSEHHMPSRLDFTLEDFLPAWEATKQLLPALADSEIEDGFNGIFSFTPDGGPLLGESKELDGFYVAEAVWVTHSAGVAKAMAELLTTGRSETDLGECDITRFEDVQLTPEYVSETSQQNFVEIYDVLHPLQPRLSPRNLRVSPFHARHKELGAFFLEAGGWERPYWFEANAALLKEMPAEWLPPARDAWSGMFSSPIAAAEAWKTRTAVAMYDMTPLKRLEVSGPGALKLLQELTTADLAKKPGAVTYTLLLDHAGGVRSAITVARLSEDTFQLGANGNIDTAYFERAARHQTQSGSATDWVQVRDTTGGTCCIGLWGPLARDLVSKVSDDDFTNDGLKYFRAKNVVIGGIPVTAMRLSYVGELGWELYTSADNGQRLWDALWQAGQPFGVIAAGRAAFSSLRLEKGYRSWGTDMTTEHDPFEAGLGFAVKMAKESFIGKGALEGRTEEASARRLRCLTIDDGRSIVLGKEPVFYKEQAVGYVTSAAYGYTVAKPIAYSYLPGTVSVGDSVDIEYFGRRITATVTEDPLYDPKMTRLRG

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	(6S)-5,6,7,8-TETRAHYDROFOLATE
Molecular weight formula_weight	445.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	1080

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6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	3gsiA01
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	3gsiA02
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	3gsiA03
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	3gsiA04
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	3gsiA05
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	71.215 Å
Unit-cell length b length_b	224.548 Å
Unit-cell length c length_c	119.382 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	2.000 Å
Low-resolution limit resolution_low	39.794 Å
R factor r_factor	0.1529
R_work r_work	0.1502
R_free r_free	0.2015

Crystal structure of D552A dimethylglycine oxidase mutant of Arthrobacter globiformis in complex with tetrahydrofolate

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

3gsi__assembly_1__model_1

3gsi__assembly_1__model_1 | I(q)

3gsi__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) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)

Crystal structure of D552A dimethylglycine oxidase mutant of Arthrobacter globiformis in complex with tetrahydrofolate

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

3gsi__assembly_1__model_1

3gsi__assembly_1__model_1 | I(q)

3gsi__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) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)