1xsj

Structure of a Family 31 alpha glycosidase

Method: X-RAY DIFFRACTION

▼

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

Putative family 31 glucosidase yicI

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 12 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YICI_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–772； UniProt 1–772 Author chain B； PDBConstruct 1–772； UniProt 1–772 Author chain C； PDBConstruct 1–772； UniProt 1–772 Author chain D； PDBConstruct 1–772； UniProt 1–772 Author chain E； PDBConstruct 1–772； UniProt 1–772 Author chain F； PDBConstruct 1–772； UniProt 1–772

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	1xsj
Deposition date deposition_date	2004-10-19
Structure title title	Structure of a Family 31 alpha glycosidase
Keywords keywords	beta(8)alpha(8) barrel and beta sandwich domains, hydrolase; HYDROLASE
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.

1xsj__assembly_1__model_1

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

Download this curve (.dat)

1xsj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xsj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	54.76 Å
Rg (electron density)	54.23 Å
Total Rg	54.58 Å
Atom count	37452
Residues	4638
Excluded volume	660860 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xsj__assembly_1__model_1`	hexameric （6）	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	Putative family 31 glucosidase yicI
Molecular weight formula_weight	89002.0 kDa
EC 编号 ec_number	3.2.1.-
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	38890

MKISDGNWLIQPGLNLIHPLQVFEVEQQDNEMVVYAAPRDVRERTWQLDTPLFTLRFFSPQEGIVGVRIEHFQGALNNGPHYPLNILQDVKVTIENTERYAEFKSGNLSARVSKGEFWSLDFLRNGERITGSQVKNNGYVQDTNNQRNYMFERLDLGVGETVYGLGERFTALVRNGQTVETWNRDGGTSTEQAYKNIPFYMTNRGYGVLVNHPQCVSFEVGSEKVSKVQFSVESEYLEYFVIDGPTPKAVLDRYTRFTGRPALPPAWSFGLWLTTSFTTNYDEATVNSFIDGMAERNLPLHVFHFDCFWMKAFQWCDFEWDPLTFPDPEGMIRRLKAKGLKICVWINPYIGQKSPVFKELQEKGYLLKRPDGSLWQWDKWQPGLAIYDFTNPDACKWYADKLKGLVAMGVDCFKTDFGERIPTDVQWFDGSDPQKMHNHYAYIYNELVWNVLKDTVGEEEAVLFARSASVGAQKFPVHWGGDCYANYESMAESLRGGLSIGLSGFGFWSHDIGGFENTAPAHVYKRWCAFGLLSSHSRLHGSKSYRVPWAYDDESCDVVRFFTQLKCRMMPYLYREAARANARGTPMMRAMMMEFPDDPACDYLDRQYMLGDNVMVAPVFTEAGDVQFYLPEGRWTHLWHNDELDGSRWHKQQHGFLSLPVYVRDNTLLALGNNDQRPDYVWHEGTAFHLFNLQDGHEAVCEVPAADGSVIFTLKAARTGNTITVTGAGEAKNWTLCLRNVVKVNGLQDGSQAESEQGLVVKPQGNALTITLHHHHHH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1438

▼

6. Fold Classification (SCOP + CATH) 54 domains

SCOP 2.08 (30 domains)

Domain ID domain_id	d1xsja1
Class class	b — All beta proteins
Fold Fold fold	b.150 — Glycolsyl hydrolase family 31 C-terminal domain-like
Superfamily Superfamily superfamily	b.150.1 — Glycolsyl hydrolase family 31 C-terminal domain
Family Family family	b.150.1.1 — Glycolsyl hydrolase family 31 C-terminal domain

Domain ID domain_id	d1xsja2
Class class	b — All beta proteins
Fold Fold fold	b.30 — Supersandwich
Superfamily Superfamily superfamily	b.30.5 — Galactose mutarotase-like
Family Family family	b.30.5.11 — Glycosyl hydrolase family 31, N-terminal domain-like

Domain ID domain_id	d1xsja3
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.71.1.4 — Glycosyl hydrolase family 31, domain 3

Domain ID domain_id	d1xsja4
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.1.8.13 — Glycosyl hydrolase family 31 catalytic domain

Domain ID domain_id	d1xsja5
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1xsjb1
Class class	b — All beta proteins
Fold Fold fold	b.150 — Glycolsyl hydrolase family 31 C-terminal domain-like
Superfamily Superfamily superfamily	b.150.1 — Glycolsyl hydrolase family 31 C-terminal domain
Family Family family	b.150.1.1 — Glycolsyl hydrolase family 31 C-terminal domain

Domain ID domain_id	d1xsjb2
Class class	b — All beta proteins
Fold Fold fold	b.30 — Supersandwich
Superfamily Superfamily superfamily	b.30.5 — Galactose mutarotase-like
Family Family family	b.30.5.11 — Glycosyl hydrolase family 31, N-terminal domain-like

Domain ID domain_id	d1xsjb3
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.71.1.4 — Glycosyl hydrolase family 31, domain 3

Domain ID domain_id	d1xsjb4
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.1.8.13 — Glycosyl hydrolase family 31 catalytic domain

Domain ID domain_id	d1xsjb5
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1xsjc1
Class class	b — All beta proteins
Fold Fold fold	b.150 — Glycolsyl hydrolase family 31 C-terminal domain-like
Superfamily Superfamily superfamily	b.150.1 — Glycolsyl hydrolase family 31 C-terminal domain
Family Family family	b.150.1.1 — Glycolsyl hydrolase family 31 C-terminal domain

Domain ID domain_id	d1xsjc2
Class class	b — All beta proteins
Fold Fold fold	b.30 — Supersandwich
Superfamily Superfamily superfamily	b.30.5 — Galactose mutarotase-like
Family Family family	b.30.5.11 — Glycosyl hydrolase family 31, N-terminal domain-like

Domain ID domain_id	d1xsjc3
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.71.1.4 — Glycosyl hydrolase family 31, domain 3

Domain ID domain_id	d1xsjc4
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.1.8.13 — Glycosyl hydrolase family 31 catalytic domain

Domain ID domain_id	d1xsjc5
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1xsjd1
Class class	b — All beta proteins
Fold Fold fold	b.150 — Glycolsyl hydrolase family 31 C-terminal domain-like
Superfamily Superfamily superfamily	b.150.1 — Glycolsyl hydrolase family 31 C-terminal domain
Family Family family	b.150.1.1 — Glycolsyl hydrolase family 31 C-terminal domain

Domain ID domain_id	d1xsjd2
Class class	b — All beta proteins
Fold Fold fold	b.30 — Supersandwich
Superfamily Superfamily superfamily	b.30.5 — Galactose mutarotase-like
Family Family family	b.30.5.11 — Glycosyl hydrolase family 31, N-terminal domain-like

Domain ID domain_id	d1xsjd3
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.71.1.4 — Glycosyl hydrolase family 31, domain 3

Domain ID domain_id	d1xsjd4
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.1.8.13 — Glycosyl hydrolase family 31 catalytic domain

Domain ID domain_id	d1xsjd5
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1xsje1
Class class	b — All beta proteins
Fold Fold fold	b.150 — Glycolsyl hydrolase family 31 C-terminal domain-like
Superfamily Superfamily superfamily	b.150.1 — Glycolsyl hydrolase family 31 C-terminal domain
Family Family family	b.150.1.1 — Glycolsyl hydrolase family 31 C-terminal domain

Domain ID domain_id	d1xsje2
Class class	b — All beta proteins
Fold Fold fold	b.30 — Supersandwich
Superfamily Superfamily superfamily	b.30.5 — Galactose mutarotase-like
Family Family family	b.30.5.11 — Glycosyl hydrolase family 31, N-terminal domain-like

Domain ID domain_id	d1xsje3
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.71.1.4 — Glycosyl hydrolase family 31, domain 3

Domain ID domain_id	d1xsje4
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.1.8.13 — Glycosyl hydrolase family 31 catalytic domain

Domain ID domain_id	d1xsje5
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1xsjf1
Class class	b — All beta proteins
Fold Fold fold	b.150 — Glycolsyl hydrolase family 31 C-terminal domain-like
Superfamily Superfamily superfamily	b.150.1 — Glycolsyl hydrolase family 31 C-terminal domain
Family Family family	b.150.1.1 — Glycolsyl hydrolase family 31 C-terminal domain

Domain ID domain_id	d1xsjf2
Class class	b — All beta proteins
Fold Fold fold	b.30 — Supersandwich
Superfamily Superfamily superfamily	b.30.5 — Galactose mutarotase-like
Family Family family	b.30.5.11 — Glycosyl hydrolase family 31, N-terminal domain-like

Domain ID domain_id	d1xsjf3
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.71.1.4 — Glycosyl hydrolase family 31, domain 3

Domain ID domain_id	d1xsjf4
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.1.8.13 — Glycosyl hydrolase family 31 catalytic domain

Domain ID domain_id	d1xsjf5
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (24 domains)

Domain ID domain_id	1xsjA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1760 — glycosyl hydrolase (family 31)

Domain ID domain_id	1xsjA02
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	1xsjA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	1xsjA04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	1xsjB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1760 — glycosyl hydrolase (family 31)

Domain ID domain_id	1xsjB02
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	1xsjB03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	1xsjB04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	1xsjC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1760 — glycosyl hydrolase (family 31)

Domain ID domain_id	1xsjC02
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	1xsjC03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	1xsjC04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	1xsjD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1760 — glycosyl hydrolase (family 31)

Domain ID domain_id	1xsjD02
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	1xsjD03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	1xsjD04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	1xsjE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1760 — glycosyl hydrolase (family 31)

Domain ID domain_id	1xsjE02
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	1xsjE03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	1xsjE04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	1xsjF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1760 — glycosyl hydrolase (family 31)

Domain ID domain_id	1xsjF02
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	1xsjF03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	1xsjF04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

▶

Unit-cell length a length_a	83.532 Å
Unit-cell length b length_b	224.442 Å
Unit-cell length c length_c	154.117 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.75 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	29.980 Å
R factor r_factor	0.1800
R_work r_work	0.1800
R_free r_free	0.2200

Structure of a Family 31 alpha glycosidase

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

Putative family 31 glucosidase yicI

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

1xsj__assembly_1__model_1

1xsj__assembly_1__model_1 | I(q)

1xsj__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) 54 domains

SCOP 2.08 (30 domains)

CATH v4.4 (24 domains)

7. Citations (1)

Structure of a Family 31 alpha glycosidase

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

Putative family 31 glucosidase yicI

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

1xsj__assembly_1__model_1

1xsj__assembly_1__model_1 | I(q)

1xsj__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) 54 domains

SCOP 2.08 (30 domains)

CATH v4.4 (24 domains)

7. Citations (1)