3ad7

Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with methylthio acetate

Method: X-RAY DIFFRACTION

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

Subunit alpha of sarcosine oxidase

Corynebacterium sp. U-96

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Subunit beta of sarcosine oxidase × 1 （Q50LF2） Subunit gamma of sarcosine oxidase × 1 （Q50LE9） Subunit delta of sarcosine oxidase × 1 （Q50LF1） NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SULFATE ION × 9 FLAVIN-ADENINE DINUCLEOTIDE × 1 FLAVIN MONONUCLEOTIDE × 1 [METHYLTHIO]ACETATE × 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	Q50LF0_9CORY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–964； UniProt 2–965

Subunit beta of sarcosine oxidase

Corynebacterium sp. U-96

UniProt Q50LF2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Subunit alpha of sarcosine oxidase × 1 （Q50LF0） Subunit gamma of sarcosine oxidase × 1 （Q50LE9） Subunit delta of sarcosine oxidase × 1 （Q50LF1） NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SULFATE ION × 9 FLAVIN-ADENINE DINUCLEOTIDE × 1 FLAVIN MONONUCLEOTIDE × 1 [METHYLTHIO]ACETATE × 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	Q50LF2_9CORY
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–404； UniProt 2–405

Subunit gamma of sarcosine oxidase

Corynebacterium sp. U-96

UniProt Q50LE9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Subunit alpha of sarcosine oxidase × 1 （Q50LF0） Subunit beta of sarcosine oxidase × 1 （Q50LF2） Subunit delta of sarcosine oxidase × 1 （Q50LF1） NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SULFATE ION × 9 FLAVIN-ADENINE DINUCLEOTIDE × 1 FLAVIN MONONUCLEOTIDE × 1 [METHYLTHIO]ACETATE × 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	Q50LE9_9CORY
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–195； UniProt 11–205

Subunit delta of sarcosine oxidase

Corynebacterium sp. U-96

UniProt Q50LF1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Subunit alpha of sarcosine oxidase × 1 （Q50LF0） Subunit beta of sarcosine oxidase × 1 （Q50LF2） Subunit gamma of sarcosine oxidase × 1 （Q50LE9） NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SULFATE ION × 9 FLAVIN-ADENINE DINUCLEOTIDE × 1 FLAVIN MONONUCLEOTIDE × 1 [METHYLTHIO]ACETATE × 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	Q50LF1_9CORY
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	3ad7
Deposition date deposition_date	2010-01-15
Structure title title	Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with methylthio acetate
Keywords keywords	Sarcosine Oxidase, Ligand Complex, 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.

3ad7__assembly_1__model_1

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

Download this curve (.dat)

3ad7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ad7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.10 Å
Rg (electron density)	35.44 Å
Total Rg	35.98 Å
Atom count	12699
Residues	1653
Excluded volume	223540 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ad7__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 (11)

Entity 1 Entity 1 polymer

Description description	Subunit alpha of sarcosine oxidase
Molecular weight formula_weight	102850.3 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	13623

SKPQRLSAAQTAGARINRDEALTLTVDGQQLSAFRGDTVASAMLANGLRSCGNSMYLDRPRGIFSAGVEEPNALITVGARHQADINESMLPATTVSVTDGLNATLLSGLGVLDPSEDPAYYDHVHVHTDVLVVGAGPAGLAAAREASRSGARVMLLDERPEAGGTLREASGEQIDGIDAAQWIDAVTEELAAAEETTHLQRTTVFGSYDANYILAAQRRTVHLDGPSGQGVSRERIWHIRAKQVVLATAAHERPIVFENNDRPGIMLAGSVRSYLNRFGVRAGSKIAVATTNDSVYPLVSELAASGGVVAVIDARQNISAAAAQAVTDGVTVLTGSVVANTEADASGELSAVLVATLDEQRNLGEAQRFEADVLAVSGGFNPVVHLHSQRQGKLNWDTSIHAFVPADAVANQHLAGALTGLLDTASALSTGAATGAAAASAAGFEKIAEVPQALAVPAGETRPVWLVPSLSGDDAVHYKFHFVDLQRDQTVADVLRATGAGMQSVEHIKRYTSISTANDQGKTSGVAAIGVIAAVLGIENPAQIGTTTFRAPYTPVSFAALAGRTRGELLDPARLTAMHPWHLAHGAKFEDVGQWKRPWYYPQDGESMDEAVYRECKAVRDSVGMLDASTLGKIEIRGKDAAEFLNRMYTNGYTKLKVGMGRYGVMCKADGMIFDDGVTLRLAEDRFLMHTTTGGAADVLDWLEEWLQTEWPELDVTCTSVTEQLATVAVVGPRSRDVIAKLASSLDVSNDAFKFMAFQDVTLDSGIEARISRISFSGELAFEIAIPAWHGLQVWEDVYAAGQEFNITPYGTETMHVLRAEKGFIIVGQDTDGTVTPQDAGMEWVVSKLKDFVGKRSFSREDNVREDRKHLVSVLPVDSSLRLAEGAALVAADAVASEGVTPMEGWVTHAYNSPALGRTFGLALIKNGRNRIGEVLKTPVDGQLVDVQVSDLVLFDPEGSRRDG

Source Source

Source organism organism	Corynebacterium sp. U-96
NCBI taxonomy ID ncbi_taxonomy_id	31944
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Subunit beta of sarcosine oxidase
Molecular weight formula_weight	44048.7 kDa
EC 编号 ec_number	1.5.3.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ADLLPEHPEFLWNNPEPKKSYDVVIVGGGGHGLATAYYLAKNHGITNVAVLEKGWLAGGNMARNTTIIRSNYLWDESAGIYEKSLKLWEELPEELEYDFLFSQRGVLNLAHTLGDVRESIRRVEANKFNGVDAEWLTPEQVKEVCPIINTGDNIRYPVMGATYQPRAGIAKHDHVAWAFARKANEMGVDIIQNCEVTGFLKDGEKVTGVKTTRGTILAGKVALAGAGHSSVLAELAGFELPIQSHPLQALVSELFEPVHPTVVMSNHIHVYVSQAHKGELVMGAGIDSYNGYGQRGAFHVIEEQMAAAVELFPIFARAHVLRTWGGIVDTTMDASPIISKTPIQNLYVNCGWGTGGFKGTPGAGYTLAHTIAHDEPHKLNAPFALERFETGHLIDEHGAAAVAH

Source Source

Source organism organism	Corynebacterium sp. U-96
NCBI taxonomy ID ncbi_taxonomy_id	31944
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Subunit gamma of sarcosine oxidase
Molecular weight formula_weight	21427.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

QLRRSPAAHLAAAMEAAEVAGERAVTLREVAFTTQLGLRAVPGSTGHAALAAATGVGLPAAVGEVAGDVSGTAVLWLGPDEFLLAAEENPALLDTLQGALGQEPGQVLDLSANRSVLQLEGPAAALVLRKSCPADLHPREFGVNRAITTSLANIPVLLWRTGEQSWRILPRASFTEHTVHWLIDAMSEFSAAEVALEHHHHHH

Source Source

Source organism organism	Corynebacterium sp. U-96
NCBI taxonomy ID ncbi_taxonomy_id	31944
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Subunit delta of sarcosine oxidase
Molecular weight formula_weight	11445.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MMLIECPNCGPRNENEFKYGGEAHVAYPEDPNALSDKEWSRYLFYRGNKKGIFAERWVHSGGCRKWFNALRDTVSYEFKAVYRAGEARPQLDSTEGGTR

Source Source

Source organism organism	Corynebacterium sp. U-96
NCBI taxonomy ID ncbi_taxonomy_id	31944
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 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 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 7 Entity 7 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 8 Entity 8 non-polymer

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

Entity 9 Entity 9 non-polymer

Description description	[METHYLTHIO]ACETATE
Molecular weight formula_weight	105.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

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

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	924

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3ad7A02
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	3ad7B01
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	3ad7B02
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	3ad7C01
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	3ad7C02
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	3ad7D00
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	198.949 Å
Unit-cell length b length_b	198.949 Å
Unit-cell length c length_c	196.765 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	39.530 Å
R factor r_factor	0.1716
R_work r_work	0.1698
R_free r_free	0.2046

Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with methylthio acetate

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

Subunit alpha of sarcosine 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

Subunit beta of sarcosine 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

Subunit gamma of sarcosine 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

Subunit delta of sarcosine 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

3ad7__assembly_1__model_1

3ad7__assembly_1__model_1 | I(q)

3ad7__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 (11)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)