SAXSdb — 1k4l

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

3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase

Magnaporthe grisea

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 × 4 MANGANESE (II) ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8TG90_MAGGR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–233； UniProt 1–233

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	1k4l
Deposition date deposition_date	2001-10-08
Structure title title	Crystal Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase in complex with two Manganese ions
Keywords keywords	dihydroxybutanone phosphate synthase, riboflavin biosynthesis, antimicrobial target, structure-based design, ISOMERASE; ISOMERASE
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.

1k4l__assembly_1__model_1

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

Download this curve (.dat)

1k4l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1k4l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.77 Å
Rg (electron density)	20.93 Å
Total Rg	21.66 Å
Atom count	3286
Residues	432
Excluded volume	57852 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1k4l__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	3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase
Molecular weight formula_weight	25036.3 kDa
EC 编号 ec_number	5.4.99.-
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	1852

MPSTDSIPKSNFDAIPDVIQAFKNGEFVVVLDDPSRENEADLIIAAESVTTEQMAFMVRHSSGLICAPLTPERTTALDLPQMVTHNADPRGTAYTVSVDAEHPSTTTGISAHDRALACRMLAAPDAQPSHFRRPGHVFPLRAVAGGVRARRGHTEAGVELCRLAGKRPVAVISEIVDDGQEVEGRAVRAAPGMLRGDECVAFARRWGLKVCTIEDMIAHVEKTEGKLETNGSG

Source Source

Source organism organism	Magnaporthe grisea
NCBI taxonomy ID ncbi_taxonomy_id	148305
Host organism host_organism	Escherichia coli BL21(DE3)

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	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	209

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1k4la_
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 (1 domains)

Domain ID domain_id	1k4lA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	870 — DHBP synthase
Homologous superfamily homologous superfamily	10 — DHBP synthase

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Unit-cell length a length_a	53.366 Å
Unit-cell length b length_b	88.346 Å
Unit-cell length c length_c	43.747 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.1990
R_free r_free	0.2670

Crystal Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase in complex with two Manganese ions

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

1k4l__assembly_1__model_1

1k4l__assembly_1__model_1 | I(q)

1k4l__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)

Crystal Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase in complex with two Manganese ions

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

1k4l__assembly_1__model_1

1k4l__assembly_1__model_1 | I(q)

1k4l__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)