SAXSdb — 3m13

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

Monomeric sarcosine oxidase

Bacillus sp.

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 CHLORIDE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1 CHLORIDE ION × 1 PHOSPHATE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1 CHLORIDE ION × 1 PHOSPHATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MSOX_BACB0
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–381； UniProt 2–382 Author chain B； PDBConstruct 1–381； UniProt 2–382 Author chain C； PDBConstruct 1–381； UniProt 2–382 Author chain D； PDBConstruct 1–381； UniProt 2–382

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	3m13
Deposition date deposition_date	2010-03-04
Structure title title	Crystal Structure of the Lys265Arg PEG-crystallized mutant of monomeric sarcosine oxidase
Keywords keywords	FLAVOPROTEIN OXIDASE, FAD, OXIDOREDUCTASE, Flavoprotein; 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.

3m13__assembly_1__model_1

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

Download this curve (.dat)

3m13__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3m13__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.44 Å
Rg (electron density)	20.49 Å
Total Rg	21.34 Å
Atom count	3032
Residues	381
Excluded volume	53514 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3m13__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3m13__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3m13__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3m13__assembly_4__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 (5)

Entity 1 Entity 1 polymer

Description description	Monomeric sarcosine oxidase
Molecular weight formula_weight	43129.4 kDa
EC 编号 ec_number	1.5.3.1
Mutation mutation	K256R
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	12635

STHFDVIVVGAGSMGMAAGYQLAKQGVKTLLVDAFDPPHTNGSHHGDTRIIRHAYGEGREYVPLALRSQELWYELEKETHHKIFTKTGVLVFGPKGESAFVAETMEAAKEHSLTVDLLEGDEINKRWPGITVPENYNAIFEPNSGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDSVKIETANGSYTADKLIVSMGAWNSKLLSKLNLDIPLQPYRQVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPSFGGCGLRLGYHTFGQKIDPDTINREFGVYPEDESNLRAFLEEYMPGANGELKRGAVCMYTKTLDEHFIIDLHPEHSNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKTEHDISIFSINRPALKESLQKTTI

Source Source

Source organism organism	Bacillus sp.
NCBI taxonomy ID ncbi_taxonomy_id	69000
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	4

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	497

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	3m13A01
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	3m13A02
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	3m13B01
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	3m13B02
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	3m13C01
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	3m13C02
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	3m13D01
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	3m13D02
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

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Unit-cell length a length_a	99.296 Å
Unit-cell length b length_b	69.298 Å
Unit-cell length c length_c	111.427 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	29.200 Å
R factor r_factor	0.1900
R_work r_work	0.1870
R_free r_free	0.2480

Crystal Structure of the Lys265Arg PEG-crystallized mutant of monomeric sarcosine oxidase

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

Monomeric sarcosine 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

3m13__assembly_1__model_1

3m13__assembly_1__model_1 | I(q)

3m13__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) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of the Lys265Arg PEG-crystallized mutant of monomeric sarcosine oxidase

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

Monomeric 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

3m13__assembly_1__model_1

3m13__assembly_1__model_1 | I(q)

3m13__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) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)