SAXSdb — 1ho1

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

;PYRIDOXINE 5'-PHOSPHATE SYNTHASE ;

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDXJ_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–242； UniProt 1–242 Author chain B； PDBConstruct 1–242； UniProt 1–242 Author chain C； PDBConstruct 1–242； UniProt 1–242 Author chain D； PDBConstruct 1–242； UniProt 1–242

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	1ho1
Deposition date deposition_date	2000-12-08
Structure title title	CRYSTAL STRUCTURE OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE
Keywords keywords	TIM barrel, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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.

1ho1__assembly_1__model_1

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

Download this curve (.dat)

1ho1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ho1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.18 Å
Rg (electron density)	36.19 Å
Total Rg	36.74 Å
Atom count	14380
Residues	1908
Excluded volume	254920 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ho1__assembly_1__model_1`	octameric （8）	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 (2)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1ho1a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.24 — Pyridoxine 5'-phosphate synthase
Family Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

Domain ID domain_id	d1ho1b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.24 — Pyridoxine 5'-phosphate synthase
Family Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

Domain ID domain_id	d1ho1c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.24 — Pyridoxine 5'-phosphate synthase
Family Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

Domain ID domain_id	d1ho1d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.24 — Pyridoxine 5'-phosphate synthase
Family Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

CATH v4.4 (4 domains)

Domain ID domain_id	1ho1A00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1ho1B00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1ho1C00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1ho1D00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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Unit-cell length a length_a	131.129 Å
Unit-cell length b length_b	155.358 Å
Unit-cell length c length_c	129.911 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	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2080
R_work r_work	0.2060
R_free r_free	0.2530

Description description	;PYRIDOXINE 5'-PHOSPHATE SYNTHASE ;
Molecular weight formula_weight	26290.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7937

CRYSTAL STRUCTURE OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE

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

;PYRIDOXINE 5'-PHOSPHATE SYNTHASE ;

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

1ho1__assembly_1__model_1

1ho1__assembly_1__model_1 | I(q)

1ho1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	747

CRYSTAL STRUCTURE OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE

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

;PYRIDOXINE 5'-PHOSPHATE SYNTHASE ;

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

1ho1__assembly_1__model_1

1ho1__assembly_1__model_1 | I(q)

1ho1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)