SAXSdb — 2jb3

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

L-AMINO ACID OXIDASE

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FLAVIN-ADENINE DINUCLEOTIDE × 2 2-AMINOBENZOIC ACID × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8VPD4_RHOOP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–489； UniProt 46–534 Author chain B； PDBConstruct 1–489； UniProt 46–534

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	2jb3
Deposition date deposition_date	2006-12-01
Structure title title	The structure of L-amino acid oxidase from Rhodococcus opacus in complex with o-aminobenzoate
Keywords keywords	;L-AMINO ACID OXIDASE, HYDRIDE TRANSFER MECHANISM, GR2-FAMILY, FLAVOENZYME, FAD CONTAINING, OXIDOREDUCTASE, INHIBITOR COMPLEX, DIMERISATION MODE ;; 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.

2jb3__assembly_1__model_1

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

Download this curve (.dat)

2jb3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2jb3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.98 Å
Rg (electron density)	30.51 Å
Total Rg	31.24 Å
Atom count	7519
Residues	954
Excluded volume	131750 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2jb3__assembly_1__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	L-AMINO ACID OXIDASE
Molecular weight formula_weight	53412.0 kDa
EC 编号 ec_number	1.4.3.2
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8511

AGDLIGKVKGSHSVVVLGGGPAGLCSAFELQKAGYKVTVLEARTRPGGRVWTARGGSEETDLSGETQKCTFSEGHFYNVGATRIPQSHITLDYCRELGVEIQGFGNQNANTFVNYQSDTSLSGQSVTYRAAKADTFGYMSELLKKATDQGALDQVLSREDKDALSEFLSDFGDLSDDGRYLGSSRRGYDSEPGAGLNFGTEKKPFAMQEVIRSGIGRNFSFDFGYDQAMMMFTPVGGMDRIYYAFQDRIGTDNIVFGAEVTSMKNVSEGVTVEYTAGGSKKSITADYAICTIPPHLVGRLQNNLPGDVLTALKAAKPSSSGKLGIEYSRRWWETEDRIYGGASNTDKDISQIMFPYDHYNSDRGVVVAYYSSGKRQEAFESLTHRQRLAKAIAEGSEIHGEKYTRDISSSFSGSWRRTKYSESAWANWAGSGGSHGGAATPEYEKLLEPVDKIYFAGDHLSNAIAWQHGALTSARDVVTHIHERVAQEA

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	2

Entity 3 Entity 3 non-polymer

Description description	2-AMINOBENZOIC ACID
Molecular weight formula_weight	137.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	985

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2jb3A01
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	2jb3A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2jb3A03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	240 —

Domain ID domain_id	2jb3B01
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	2jb3B02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2jb3B03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	240 —

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Unit-cell length a length_a	65.649 Å
Unit-cell length b length_b	109.676 Å
Unit-cell length c length_c	134.368 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	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	19.770 Å
R factor r_factor	0.1540
R_work r_work	0.1510
R_free r_free	0.2140

The structure of L-amino acid oxidase from Rhodococcus opacus in complex with o-aminobenzoate

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

L-AMINO ACID 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

2jb3__assembly_1__model_1

2jb3__assembly_1__model_1 | I(q)

2jb3__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (2)

The structure of L-amino acid oxidase from Rhodococcus opacus in complex with o-aminobenzoate

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

L-AMINO ACID 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

2jb3__assembly_1__model_1

2jb3__assembly_1__model_1 | I(q)

2jb3__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (2)