SAXSdb — 1g58

▼

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

3,4-DIHYDROXY-2-BUTANONE 4-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 2	GOLD ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RIBB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–217； UniProt 1–217 Author chain B； PDBConstruct 1–217； UniProt 1–217

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1g58
Deposition date deposition_date	2000-10-30
Structure title title	CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE GOLD DERIVATIVE
Keywords keywords	;dihydroxybutanone phosphate synthase, riboflavin biosynthesis, skeletal rearrangement, antimicrobial target, structure-based design, ISOMERASE ;; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1g58__assembly_1__model_1

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

Download this curve (.dat)

1g58__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1g58__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.99 Å
Rg (electron density)	21.23 Å
Total Rg	21.83 Å
Atom count	2926
Residues	392
Excluded volume	51987 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1g58__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE
Molecular weight formula_weight	23335.4 kDa
EC 编号 ec_number	5.4.99.-
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	3225

MAQTLLSSFGTPFERVENALAALREGRGVMVLDDEDRENEGDMIFPAETMTVEQMALTIRHGSGIVCLCITEDRRKQLDLPMMVENNTSAYGTGFTVTIEAAEGVTTGVSAADRITTVRAAIADGAKPSDLNRPGHVFPLRAQAGGVLTRGGHTEATIDLMTLAGFKPAGVLCELTNDDGTMARAPECIEFANKHNMALVTIEDLVAYRQAHERKAS

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	GOLD ION
Molecular weight formula_weight	197.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	299

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1g58a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.115 — YrdC/RibB
Superfamily Superfamily superfamily	d.115.1 — YrdC/RibB
Family Family family	d.115.1.2 — 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB

Domain ID domain_id	d1g58b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.115 — YrdC/RibB
Superfamily Superfamily superfamily	d.115.1 — YrdC/RibB
Family Family family	d.115.1.2 — 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB

CATH v4.4 (2 domains)

Domain ID domain_id	1g58A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	870 — DHBP synthase
Homologous superfamily homologous superfamily	10 — DHBP synthase

Domain ID domain_id	1g58B00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	870 — DHBP synthase
Homologous superfamily homologous superfamily	10 — DHBP synthase

▶

Unit-cell length a length_a	78.220 Å
Unit-cell length b length_b	78.220 Å
Unit-cell length c length_c	69.880 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
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	—
R_work r_work	0.1850
R_free r_free	0.2310

CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE GOLD DERIVATIVE

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

3,4-DIHYDROXY-2-BUTANONE 4-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

1g58__assembly_1__model_1

1g58__assembly_1__model_1 | I(q)

1g58__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE GOLD DERIVATIVE

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

3,4-DIHYDROXY-2-BUTANONE 4-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

1g58__assembly_1__model_1

1g58__assembly_1__model_1 | I(q)

1g58__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)