SAXSdb — 3vgd

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

Malto-oligosyltrehalose trehalohydrolase

Sulfolobus solfataricus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CITRATE ANION × 1 GLYCEROL × 5 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	CITRATE ANION × 2 GLYCEROL × 10 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TREZ_SULSF
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–558； UniProt 2–559

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	3vgd
Deposition date deposition_date	2011-08-09
Structure title title	Ctystal structure of glycosyltrehalose trehalohydrolase (D252E)
Keywords keywords	alpha/beta barrel, trehalose, trehalohydrolase, alpha-amylase, HYDROLASE; HYDROLASE
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.

3vgd__assembly_1__model_1

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

Download this curve (.dat)

3vgd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3vgd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.64 Å
Rg (electron density)	24.76 Å
Total Rg	25.65 Å
Atom count	4580
Residues	553
Excluded volume	81441 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3vgd__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3vgd__assembly_2__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	Malto-oligosyltrehalose trehalohydrolase
Molecular weight formula_weight	64755.8 kDa
EC 编号 ec_number	3.2.1.141
Mutation mutation	D252E
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	4972

TFAYKIDGNEVIFTLWAPYQKSVKLKVLEKGLYEMERDEKGYFTITLNNVKVRDRYKYVLDDASEIPDPASRYQPEGVHGPSQIIQESKEFNNETFLKKEDLIIYEIHVGTFTPEGTFEGVIRKLDYLKDLGITAIEIMPIAQFPGKRDWGYDGVYLYAVQNSYGGPEGFRKLVDEAHKKGLGVILDVVYNHVGPEGNYMVKLGPYFSQKYKTPWGLTFNFDDAESDEVRKFILENVEYWIKEYNVDGFRLEAVHAIIDTSPKHILEEIADVVHKYNRIVIAESDLNDPRVVNPKEKCGYNIDAQWVDDFHHSIHAYLTGERQGYYTDFGNLDDIVKSYKDVFVYDGKYSNFRRKTHGEPVGELDGCNFVVYIQNHDQVGNRGKGERIIKLVDRESYKIAAALYLLSPYIPMIFMGEEYGEENPFYFFSDFSDSKLIQGVREGRKKENGQDTDPQDESTFNASKLSWKIDEEIFSFYKILIKMRKELSIACDRRVNVVNGENWLIIKGREYFSLYVFSKSSIEVKYSGTLLLSSNNSFPQHIEEGKYEFDKGFALYKL

Source Source

Source organism organism	Sulfolobus solfataricus
NCBI taxonomy ID ncbi_taxonomy_id	2287
Host organism host_organism	Pichia jadinii

Entity 2 Entity 2 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	392

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3vgda1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.2 — E-set domains of sugar-utilizing enzymes

Domain ID domain_id	d3vgda2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.1 — Amylase, catalytic domain

Domain ID domain_id	d3vgda3
Class class	b — All beta proteins
Fold Fold fold	b.71 — Glycosyl hydrolase domain
Superfamily Superfamily superfamily	b.71.1 — Glycosyl hydrolase domain
Family Family family	b.71.1.1 — alpha-Amylases, C-terminal beta-sheet domain

CATH v4.4 (3 domains)

Domain ID domain_id	3vgdA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3vgdA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	3vgdA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

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Unit-cell length a length_a	78.881 Å
Unit-cell length b length_b	78.881 Å
Unit-cell length c length_c	282.530 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 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	61.500 Å
R factor r_factor	0.1601
R_work r_work	0.1581
R_free r_free	0.1983

Ctystal structure of glycosyltrehalose trehalohydrolase (D252E)

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

Malto-oligosyltrehalose trehalohydrolase

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

3vgd__assembly_1__model_1

3vgd__assembly_1__model_1 | I(q)

3vgd__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Ctystal structure of glycosyltrehalose trehalohydrolase (D252E)

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

Malto-oligosyltrehalose trehalohydrolase

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

3vgd__assembly_1__model_1

3vgd__assembly_1__model_1 | I(q)

3vgd__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)