SAXSdb — 3ahe

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

Xylulose 5-phosphate/fructose 6-phosphate phosphoketolase

Bifidobacterium breve

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 2-[3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-2-(1,2-DIHYDROXYETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE × 2 SODIUM ION × 2 1,2-ETHANEDIOL × 22 NONAETHYLENE GLYCOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D6PAH1_BIFBR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–845； UniProt 1–825

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	3ahe
Deposition date deposition_date	2010-04-22
Structure title title	Phosphoketolase from Bifidobacterium Breve complexed with dihydroxyethyl thiamine diphosphate
Keywords keywords	THIAMINE DIPHOSPHATE-DEPENDENT ENZYME, ALPHA-BETA FOLD, HOMODIMER, DIHYDROXYETHYL THIAMINE DIPHOSPHATE, LYASE; LYASE
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.

3ahe__assembly_1__model_1

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

Download this curve (.dat)

3ahe__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ahe__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.60 Å
Rg (electron density)	32.69 Å
Total Rg	33.34 Å
Atom count	12966
Residues	1604
Excluded volume	228760 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ahe__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 (7)

Entity 1 Entity 1 polymer

Description description	Xylulose 5-phosphate/fructose 6-phosphate phosphoketolase
Molecular weight formula_weight	94962.9 kDa
EC 编号 ec_number	4.1.2.22
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	7280

MGSSHHHHHHSSGLVPRGSHMTNPVIGTPWQKLDRPVSEEAIEGMDKYWRVTNYMSIGQIYLRSNPLMKEPFTRDDVKHRLVGHWGTTPGLNFLLAHINRLIADHQQNTVFIMGPGHGGPAGTSQSYVDGTYTEYYPNITKDEAGLQKFFRQFSYPGGIPSHFAPETPGSIHEGGELGYALSHAYGAVMNNPSLFVPCIIGDGEAETGPLATGWQSNKLVNPRTDGIVLPILHLNGYKIANPTILARISDEELHDFFRGMGYHPYEFVAGFDNEDHMSIHRRFAELFETIFDEICDIKAAAQTDDMTRPFYPMLIFRTPKGWTCPKFIDGKKTEGSWRAHQVPLASARDTEEHFEVLKGWMESYKPEELFNADGSIKDDVTAFMPKGELRIGANPNANGGVIREDLKLPELDQYEVTGVKEYGHGWGQVEAPRALGAYCRDIIKNNPDSFRIFGPDETASNRLNATYEVTDKQWDNGYLSGLVDEHMAVTGQVTEQLSEHQCEGFLEAYLLTGRHGIWSSYESFVHVIDSMLNQHAKWLEATVREIPWRKPISSVNLLVSSHVWRQDHNGFSHQDPGVTSLLINKTFNNDHVTNIYFATDANMLLAISEKCFKSTNKINAIFAGKQPAPTWVTLDEARAELEAGAAEWKWASNAENNDEVQVVLASAGDVPTQELMAASDALNKMGIKFKVVNVVDLLKLQSRENNDEALTDEEFTELFTADKPVLFAYHSYAQDVRGLIYDRPNHDNFHVVGYKEQGSTTTPFDMVRVNDMDRYALQAAALKLIDADKYADKIDELNAFRKKAFQFAVDNGYDIPEFTDWVYPDVKVDETQMLSATAATAGDNE

Source Source

Source organism organism	Bifidobacterium breve
NCBI taxonomy ID ncbi_taxonomy_id	1685
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	1

Entity 3 Entity 3 non-polymer

Description description	2-[3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-2-(1,2-DIHYDROXYETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE
Molecular weight formula_weight	484.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 6 Entity 6 non-polymer

Description description	NONAETHYLENE GLYCOL
Molecular weight formula_weight	414.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	797

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3aheA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	3aheA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	3aheA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	920 —

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Unit-cell length a length_a	173.529 Å
Unit-cell length b length_b	173.529 Å
Unit-cell length c length_c	163.516 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	16

Space group space_group	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	49.070 Å
R factor r_factor	0.1629
R_work r_work	0.1607
R_free r_free	0.2064

Phosphoketolase from Bifidobacterium Breve complexed with dihydroxyethyl thiamine diphosphate

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

Xylulose 5-phosphate/fructose 6-phosphate phosphoketolase

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

3ahe__assembly_1__model_1

3ahe__assembly_1__model_1 | I(q)

3ahe__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (2)

Phosphoketolase from Bifidobacterium Breve complexed with dihydroxyethyl thiamine diphosphate

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

Xylulose 5-phosphate/fructose 6-phosphate phosphoketolase

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

3ahe__assembly_1__model_1

3ahe__assembly_1__model_1 | I(q)

3ahe__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (2)