SAXSdb — 1yxo

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

4-hydroxythreonine-4-phosphate dehydrogenase 1

Pseudomonas aeruginosa

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 ETHANOL × 10 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDXA1_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–328； UniProt 1–328 Author chain B； PDBConstruct 1–328； UniProt 1–328

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	1yxo
Deposition date deposition_date	2005-02-22
Structure title title	Crystal Structure of pyridoxal phosphate biosynthetic protein PdxA PA0593
Keywords keywords	;PA0593, PYRIDOXINE BIOSYNTHESIS, OXIDOREDUCTASE, Structural Genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG ;; 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.

1yxo__assembly_1__model_1

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

Download this curve (.dat)

1yxo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yxo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.96 Å
Rg (electron density)	28.27 Å
Total Rg	28.72 Å
Atom count	4942
Residues	644
Excluded volume	88545 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yxo__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	4-hydroxythreonine-4-phosphate dehydrogenase 1
Molecular weight formula_weight	35247.7 kDa
EC 编号 ec_number	1.1.1.262
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	5392

MSLRFALTPGEPAGIGPDLCLLLARSAQPHPLIAIASRTLLQERAGQLGLAIDLKDVSPAAWPERPAKAGQLYVWDTPLAAPVRPGQLDRANAAYVLETLTRAGQGCLDGHFAGMITAPVHKGVINEAGIPFSGHTEFLADLTHTAQVVMMLATRGLRVALATTHLPLREVADAISDERLTRVARILHADLRDKFGIAHPRILVCGLNPHAGEGGHLGREEIEVIEPCLERLRGEGLDLIGPLPADTLFTPKHLEHCDAVLAMYHDQGLPVLKYKGFGAAVNVTLGLPIIRTSVDHGTALDLAGSGRIDSGSLQVALETAYQMAASRC

Source Source

Source organism organism	Pseudomonas aeruginosa
NCBI taxonomy ID ncbi_taxonomy_id	287
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ETHANOL
Molecular weight formula_weight	46.1 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	450

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1yxoa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
Family Family family	c.77.1.3 — PdxA-like

Domain ID domain_id	d1yxob_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
Family Family family	c.77.1.3 — PdxA-like

CATH v4.4 (2 domains)

Domain ID domain_id	1yxoA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	718 — Isopropylmalate Dehydrogenase
Homologous superfamily homologous superfamily	10 — Isopropylmalate Dehydrogenase

Domain ID domain_id	1yxoB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	718 — Isopropylmalate Dehydrogenase
Homologous superfamily homologous superfamily	10 — Isopropylmalate Dehydrogenase

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Unit-cell length a length_a	54.259 Å
Unit-cell length b length_b	59.307 Å
Unit-cell length c length_c	199.111 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	2.010 Å
Low-resolution limit resolution_low	36.680 Å
R factor r_factor	0.1980
R_work r_work	0.1980
R_free r_free	0.2430

Crystal Structure of pyridoxal phosphate biosynthetic protein PdxA PA0593

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

4-hydroxythreonine-4-phosphate dehydrogenase 1

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

1yxo__assembly_1__model_1

1yxo__assembly_1__model_1 | I(q)

1yxo__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of pyridoxal phosphate biosynthetic protein PdxA PA0593

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

4-hydroxythreonine-4-phosphate dehydrogenase 1

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

1yxo__assembly_1__model_1

1yxo__assembly_1__model_1 | I(q)

1yxo__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)