2gag

Heteroteterameric sarcosine: structure of a diflavin metaloenzyme at 1.85 a resolution

Method: X-RAY DIFFRACTION

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

heterotetrameric sarcosine oxidase alpha-subunit

Stenotrophomonas maltophilia

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	heterotetrameric sarcosine oxidase beta-subunit × 1 heterotetrameric sarcosine oxidase gamma-subunit × 1 heterotetrameric sarcosine oxidase delta-subunit × 1 （Q3ZDQ9） 2-FUROIC ACID × 2 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 GLYCEROL × 1 SULFITE ION × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 FLAVIN MONONUCLEOTIDE × 1 ZINC ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3ZDQ8_XANMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–965； UniProt 1–965

heterotetrameric sarcosine oxidase delta-subunit

Stenotrophomonas maltophilia

UniProt Q3ZDQ9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	heterotetrameric sarcosine oxidase alpha-subunit × 1 （Q3ZDQ8） heterotetrameric sarcosine oxidase beta-subunit × 1 heterotetrameric sarcosine oxidase gamma-subunit × 1 2-FUROIC ACID × 2 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 GLYCEROL × 1 SULFITE ION × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 FLAVIN MONONUCLEOTIDE × 1 ZINC ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3ZDQ9_XANMA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–99； UniProt 1–99

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	2gag
Deposition date deposition_date	2006-03-08
Structure title title	Heteroteterameric sarcosine: structure of a diflavin metaloenzyme at 1.85 a resolution
Keywords keywords	Sarcosine oxidase, Flavoenzyme, Electron transfer, Folate-methylating enzyme, 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.

2gag__assembly_1__model_1

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

Download this curve (.dat)

2gag__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2gag__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.05 Å
Rg (electron density)	35.39 Å
Total Rg	35.94 Å
Atom count	12657
Residues	1649
Excluded volume	222930 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2gag__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 (12)

Entity 1 Entity 1 polymer

Description description	heterotetrameric sarcosine oxidase alpha-subunit
Molecular weight formula_weight	103218.5 kDa
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	14136

MSKPQRLSAEQSSRARINREEALSLTVDGAKLSAFRGDTVASALLANGVRRAGNSLYLDRPRGIFAAGVEEPNALVTVSARHEQDIDESMLPATTVPVTEDLNATLLSGLGVLDPTKDPAYYDHVHVHTDVLVVGAGPAGLAAAREASRSGARVMLLDERAEAGGTLLDTAGEQIDGMDSSAWIEQVTSELAEAEETTHLQRTTVFGSYDANYLIAAQRRTVHLDGPSGPGVSRERIWHIRAKQVVLATGAHERPIVFENNDRPGIMLAGAVRSYLNRYGVRAGARIAVATTNDSAYELVRELAATGGVVAVIDARSSISAAAAQAVADGVQVISGSVVVDTEADENGELSAIVVAELDEARELGGTQRFEADVLAVAGGFNPVVHLHSQRQGKLDWDTTIHAFVPADAVANQHLAGAMTGRLDTASALSTGAATGAAAATAAGFATVARTPQALETALGETRPVWLVPSVSGDDAVNYKFHFVDLQRDQTVADVLRATGAGMKSVEHIKRYTSISTANDQGKTSGVAAIGVIAAVLGIENPAAIGTTTFRAPYTPVAFAALAGRNRGDQLDPARITAMHSWHLSHGAEFEDVGQWKRPWYYPQAGETMDQAVYRESKAVRDSVGMLDATTLGKIEIRGKDAAEFLNRIYTNGYTKLKVGMGRYGVMCKADGMIFDDGVTLRLAEDRFLLHTTTGGAADVLDWLEEWLQTEWPDLDVTCTSVTEQLATVAVVGPRSRDVIAKLASTVDVSNEGFKFMAFKDVVLDSGIEARISRISFSGELAFEIAVPAWHGLRVWEDVYAAGEEFNITPYGTETMHVLRAEKGFIIVGQDTDGTVTPQDAGMEWVVSKLKDFIGNRSYSRADNAREDRKQLVSVLPVDKSLRLPEGAALVASDALASEGITPMEGWVTSSYDSPNLGRTFGLALIKNGRNRIGEVLKTPVGDQLVDVVVSETVLYDPEGSRRDG

Source Source

Source organism organism	Stenotrophomonas maltophilia
NCBI taxonomy ID ncbi_taxonomy_id	40324
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	heterotetrameric sarcosine oxidase beta-subunit
Molecular weight formula_weight	44117.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MADLLPEHPEFLWANPEPKKSYDAIIVGGGGHGLATAYFLAKNHGITNVAVLEKGWLAGGNMARNTTIIRSNYLWDESAGIYEKSLKLWEQLPEDLEYDFLFSQRGVLNLAHTLGDVRESVRRVEANKLNGVDAEWLDPSQVKEACPIINTSDDIRYPVMGATWQPRAGIAKHDHVAWAFARKANEMGVDIIQNCEVTGFIKDGEKVTGVKTTRGTIHAGKVALAGAGHSSVLAEMAGFELPIQSHPLQALVSELFEPVHPTVVMSNHIHVYVSQAHKGELVMGAGIDSYNGYGQRGAFHVIQEQMAAAVELFPIFARAHVLRTWGGIVDTTMDASPIISKTPIQNLYVNCGWGTGGFKGTPGAGFTLAHTIANDEPHELNKPFSLERFETGHLIDEHGAAAVAH

Source Source

Source organism organism	Stenotrophomonas maltophilia
NCBI taxonomy ID ncbi_taxonomy_id	40324
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 polymer

Description description	heterotetrameric sarcosine oxidase gamma-subunit
Molecular weight formula_weight	22235.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MANNTLIETPLRHSPAEHLDTVMDAASVAGRVELREIAFTTQISLRCAPGTQAHAALAAATGAGLPAKVGEVAGEAQGTAVLWLAPDEFLATSAENTELGGVLSAALGDAPGQVVDLSANRSVLELTGPDAPLVLRKSCPADLHPRAFAVNQAIVTSVANIPVLLWRTGEQAWRIMPRASFTEHTVHWLVDAMSEFASEAVILEHHHHHH

Source Source

Source organism organism	Stenotrophomonas maltophilia
NCBI taxonomy ID ncbi_taxonomy_id	40324
Host organism host_organism	Escherichia coli BL21

Entity 4 Entity 4 polymer

Description description	heterotetrameric sarcosine oxidase delta-subunit
Molecular weight formula_weight	11395.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MMLIDCPNCGPRNENEFKYGGEAHVAYPADPHALSDKQWSRYLFYRQNKKGIFAERWVHAAGCRKWFNALRDTVTYEFKAIYPAGAPRPEIHSAEGGTR

Source Source

Source organism organism	Stenotrophomonas maltophilia
NCBI taxonomy ID ncbi_taxonomy_id	40324
Host organism host_organism	Escherichia coli BL21

Entity 5 Entity 5 non-polymer

Description description	2-FUROIC ACID
Molecular weight formula_weight	112.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	SULFITE ION
Molecular weight formula_weight	80.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 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 10 Entity 10 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1479

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2gagA02
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	2gagB01
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	2gagB02
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	2gagC01
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	2gagC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1520 — Heterotetrameric sarcosine oxidase

Domain ID domain_id	2gagD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2270 — Folate-binding fold
Homologous superfamily homologous superfamily	10 — Folate-binding superfamily

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Unit-cell length a length_a	73.186 Å
Unit-cell length b length_b	132.407 Å
Unit-cell length c length_c	197.418 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	—
R_work r_work	0.1890
R_free r_free	0.2300

Heteroteterameric sarcosine: structure of a diflavin metaloenzyme at 1.85 a resolution

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

heterotetrameric sarcosine oxidase alpha-subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

heterotetrameric sarcosine oxidase delta-subunit

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

2gag__assembly_1__model_1

2gag__assembly_1__model_1 | I(q)

2gag__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 (12)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (2)