SAXSdb — 4pfh

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

D-tagatose 3-epimerase

Pseudomonas cichorii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 3 D-psicose × 2 D-fructose × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DT3E_PSECI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–290； UniProt 1–290 Author chain B； PDBConstruct 1–290； UniProt 1–290

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	4pfh
Deposition date deposition_date	2014-04-29
Structure title title	Crystal structure of engineered D-tagatose 3-epimerase PcDTE-IDF8
Keywords keywords	epimerase, TIM-barrel, 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.

4pfh__assembly_1__model_1

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

Download this curve (.dat)

4pfh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4pfh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.59 Å
Rg (electron density)	24.68 Å
Total Rg	25.46 Å
Atom count	4714
Residues	589
Excluded volume	83609 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4pfh__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 (5)

Entity 1 Entity 1 polymer

Description description	D-tagatose 3-epimerase
Molecular weight formula_weight	33922.6 kDa
EC 编号 ec_number	5.3.1.-
Mutation mutation	S37N,G39E,T109N,S116H,K122V,F157Y,T194N,H209V,L212I,K251T,S256G,A258D,G260C,M265L
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	5285

MNKVGMFYTYWSTEWMVDFPATAKRIAGLGFDLMEINLEEFHNLSDAKKRELKAVADDLGLTVMCCIGLKSEYDFASPDKSVRDAGTEYVKRLLDDCHLLGAPVFAGLNFCAWPQHPPLDMVDKRPYVDRAIESVRRVIKVAEDYGIIYALEVVNRYEQWLCNDAKEAIAFADAVDSPACKVQLDTFHMNIEENSFRDAILACKGKMGVFHIGEQNRLPPGEGRLPWDEIFGALKEIGYDGTIVMEPFMRTGGSVGRDVCVWRDLSNGATDEEMDERARRSLQFVRDKLALEHHHHHH

Source Source

Source organism organism	Pseudomonas cichorii
NCBI taxonomy ID ncbi_taxonomy_id	36746
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	D-psicose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	D-fructose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	411

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4pfhA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	150 — Divalent-metal-dependent TIM barrel enzymes

Domain ID domain_id	4pfhB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	150 — Divalent-metal-dependent TIM barrel enzymes

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Unit-cell length a length_a	57.460 Å
Unit-cell length b length_b	86.740 Å
Unit-cell length c length_c	61.820 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	56.740 Å
R factor r_factor	0.1460
R_work r_work	0.1440
R_free r_free	0.1770

Crystal structure of engineered D-tagatose 3-epimerase PcDTE-IDF8

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

D-tagatose 3-epimerase

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

4pfh__assembly_1__model_1

4pfh__assembly_1__model_1 | I(q)

4pfh__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of engineered D-tagatose 3-epimerase PcDTE-IDF8

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

D-tagatose 3-epimerase

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

4pfh__assembly_1__model_1

4pfh__assembly_1__model_1 | I(q)

4pfh__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)