SAXSdb — 1dnl

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

;PYRIDOXINE 5'-PHOSPHATE OXIDASE ;

Escherichia coli K12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 2 FLAVIN MONONUCLEOTIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDXH_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–199； UniProt 19–217

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	1dnl
Deposition date deposition_date	1999-12-16
Structure title title	X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE COMPLEXED WITH FMN AT 1.8 ANGSTROM RESOLUTION
Keywords keywords	BETA BARREL, PROTEIN-FMN 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.

1dnl__assembly_1__model_1

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

Download this curve (.dat)

1dnl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1dnl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.95 Å
Rg (electron density)	22.02 Å
Total Rg	22.82 Å
Atom count	3356
Residues	390
Excluded volume	59410 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1dnl__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	;PYRIDOXINE 5'-PHOSPHATE OXIDASE ;
Molecular weight formula_weight	23439.2 kDa
EC 编号 ec_number	1.4.3.5
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	1824

GGLRRRDLPADPLTLFERWLSQACEAKLADPTAMVVATVDEHGQPYQRIVLLKHYDEKGMVFYTNLGSRKAHQIENNPRVSLLFPWHTLERQVMVIGKAERLSTLEVMKYFHSRPRDSQIGAWVSKQSSRISARGILESKFLELKQKFQQGEVPLPSFWGGFRVSLEQIEFWQGGEHRLHDRFLYQRENDAWKIDRLAP

Source Source

Source organism organism	Escherichia coli K12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1dnla_
Class class	b — All beta proteins
Fold Fold fold	b.45 — Split barrel-like
Superfamily Superfamily superfamily	b.45.1 — FMN-binding split barrel
Family Family family	b.45.1.1 — PNP-oxidase like

CATH v4.4 (1 domains)

Domain ID domain_id	1dnlA00
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	63.710 Å
Unit-cell length b length_b	63.710 Å
Unit-cell length c length_c	125.250 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	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	55.000 Å
R factor r_factor	0.2120
R_work r_work	0.2100
R_free r_free	0.2330

X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE COMPLEXED WITH FMN AT 1.8 ANGSTROM RESOLUTION

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

;PYRIDOXINE 5'-PHOSPHATE 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

1dnl__assembly_1__model_1

1dnl__assembly_1__model_1 | I(q)

1dnl__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

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE COMPLEXED WITH FMN AT 1.8 ANGSTROM RESOLUTION

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

;PYRIDOXINE 5'-PHOSPHATE 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

1dnl__assembly_1__model_1

1dnl__assembly_1__model_1 | I(q)

1dnl__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

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)