SAXSdb — 3ba3

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

;Pyridoxamine 5'-phosphate oxidase-like protein ;

Lactobacillus plantarum WCFS1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 1,2-ETHANEDIOL × 10 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q890D6_LACPL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–145； UniProt 1–144 Author chain B； PDBConstruct 2–145； UniProt 1–144

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	3ba3
Deposition date deposition_date	2007-11-07
Structure title title	Crystal structure of Pyridoxamine 5'-phosphate oxidase-like protein (NP_783940.1) from Lactobacillus plantarum at 1.55 A resolution
Keywords keywords	;NP_783940.1, Pyridoxamine 5'-phosphate oxidase-like protein, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, 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.

3ba3__assembly_1__model_1

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

Download this curve (.dat)

3ba3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ba3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.37 Å
Rg (electron density)	19.13 Å
Total Rg	20.16 Å
Atom count	2278
Residues	283
Excluded volume	40906 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ba3__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	;Pyridoxamine 5'-phosphate oxidase-like protein ;
Molecular weight formula_weight	16207.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2828

GMDISLLKQVVQSTNKIALSTAVNNEADVKIVNFVWYEAQPDTLYFSSVKTSPALKVYDQNPDIAFITIPNDGTAGNPYLRAQHVKLQRSTKTMTDLLPQYLETVPNYQQVWDAIGSTLVVFELKLTDLFVDAGVGGEKQTLTFN

Source Source

Source organism organism	Lactobacillus plantarum WCFS1
NCBI taxonomy ID ncbi_taxonomy_id	220668
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	413

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3ba3A00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	110 — Pnp Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Electron Transport, Fmn-binding Protein; Chain A

Domain ID domain_id	3ba3B00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	110 — Pnp Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Electron Transport, Fmn-binding Protein; Chain A

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Unit-cell length a length_a	137.379 Å
Unit-cell length b length_b	137.379 Å
Unit-cell length c length_c	137.379 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	48

Space group space_group	P 43 3 2
Space-group number int_tables_number	212
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	29.975 Å
R factor r_factor	0.1710
R_work r_work	0.1700
R_free r_free	0.1960

Crystal structure of Pyridoxamine 5'-phosphate oxidase-like protein (NP_783940.1) from Lactobacillus plantarum at 1.55 A resolution

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

;Pyridoxamine 5'-phosphate oxidase-like protein ;

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

3ba3__assembly_1__model_1

3ba3__assembly_1__model_1 | I(q)

3ba3__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

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Pyridoxamine 5'-phosphate oxidase-like protein (NP_783940.1) from Lactobacillus plantarum at 1.55 A resolution

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

;Pyridoxamine 5'-phosphate oxidase-like protein ;

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

3ba3__assembly_1__model_1

3ba3__assembly_1__model_1 | I(q)

3ba3__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

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)