2f2h

Structure of the YicI thiosugar Michaelis complex

Method: X-RAY DIFFRACTION

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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	SULFATE ION × 9 4-NITROPHENYL 6-THIO-6-S-ALPHA-D-XYLOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE × 7 GLYCEROL × 14 3[N-MORPHOLINO]PROPANE SULFONIC ACID × 5 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2f2h
Deposition date deposition_date	2005-11-16
Structure title title	Structure of the YicI thiosugar Michaelis complex
Keywords keywords	beta8alpha8 barrel, 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.

2f2h__assembly_1__model_1

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

Download this curve (.dat)

2f2h__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2f2h__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	55.04 Å
Rg (electron density)	54.45 Å
Total Rg	54.81 Å
Atom count	37796
Residues	4638
Excluded volume	666530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2f2h__assembly_1__model_1`	hexameric （6）	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 (6)

Entity 1 Entity 1 polymer

Description description	Putative family 31 glucosidase yicI
Molecular weight formula_weight	88311.3 kDa
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	39799

MKISDGNWLIQPGLNLIHPLQVFEVEQQDNEMVVYAAPRDVRERTWQLDTPLFTLRFFSPQEGIVGVRIEHFQGALNNGPHYPLNILQDVKVTIENTERYAEFKSGNLSARVSKGEFWSLDFLRNGERITGSQVKNNGYVQDTNNQRNYMFERLDLGVGETVYGLGERFTALVRNGQTVETWNRDGGTSTEQAYKNIPFYMTNRGYGVLVNHPQCVSFEVGSEKVSKVQFSVESEYLEYFVIDGPTPKAVLDRYTRFTGRPALPPAWSFGLWLTTSFTTNYDEATVNSFIDGMAERNLPLHVFHFDCFWMKAFQWCDFEWDPLTFPDPEGMIRRLKAKGLKICVWINPYIGQKSPVFKELQEKGYLLKRPDGSLWQWDKWQPGLAIYDFTNPDACKWYADKLKGLVAMGVDCFKTDFGERIPTDVQWFDGSDPQKMHNHYAYIYNELVWNVLKDTVGEEEAVLFARSASVGAQKFPVHWGGDCYANYESMAESLRGGLSIGLSGFGFWSHDIGGFENTAPAHVYKRWCAFGLLSSHSRLHGSKSYRVPWAYDDESCDVVRFFTQLKCRMMPYLYREAARANARGTPMMRAMMMEFPDDPACDYLDRQYMLGDNVMVAPVFTEAGDVQFYLPEGRWTHLWHNDELDGSRWHKQQHGFLSLPVYVRDNTLLALGNNDQRPDYVWHEGTAFHLFNLQDGHEAVCEVPAADGSVIFTLKAARTGNTITVTGAGEAKNWTLCLRNVVKVNGLQDGSQAESEQGLVVKPQGNALTITLH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
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	9

Entity 3 Entity 3 non-polymer

Description description	4-NITROPHENYL 6-THIO-6-S-ALPHA-D-XYLOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE
Molecular weight formula_weight	449.4 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 5 Entity 5 non-polymer

Description description	3[N-MORPHOLINO]PROPANE SULFONIC ACID
Molecular weight formula_weight	209.3 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2003

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6. Fold Classification (SCOP + CATH) 54 domains

SCOP 2.08 (30 domains)

Domain ID domain_id	d2f2ha1
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	d2f2ha2
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	d2f2ha3
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	d2f2ha4
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	d2f2ha5
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	d2f2hb1
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	d2f2hb2
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	d2f2hb3
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	d2f2hb4
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	d2f2hb5
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	d2f2hc1
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	d2f2hc2
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	d2f2hc3
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	d2f2hc4
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	d2f2hc5
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	d2f2hd1
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	d2f2hd2
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	d2f2hd3
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	d2f2hd4
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	d2f2hd5
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	d2f2he1
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	d2f2he2
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	d2f2he3
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	d2f2he4
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	d2f2he5
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	d2f2hf1
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	d2f2hf2
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	d2f2hf3
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	d2f2hf4
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	d2f2hf5
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	2f2hA01
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	2f2hA02
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	2f2hA03
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	2f2hA04
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	2f2hB01
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	2f2hB02
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	2f2hB03
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	2f2hB04
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	2f2hC01
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	2f2hC02
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	2f2hC03
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	2f2hC04
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	2f2hD01
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	2f2hD02
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	2f2hD03
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	2f2hD04
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	2f2hE01
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	2f2hE02
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	2f2hE03
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	2f2hE04
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	2f2hF01
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	2f2hF02
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	2f2hF03
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	2f2hF04
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	162.317 Å
Unit-cell length b length_b	175.841 Å
Unit-cell length c length_c	210.742 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	28.640 Å
R factor r_factor	0.1820
R_work r_work	0.1800
R_free r_free	0.2250

Structure of the YicI thiosugar Michaelis complex

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

2f2h__assembly_1__model_1

2f2h__assembly_1__model_1 | I(q)

2f2h__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 54 domains

SCOP 2.08 (30 domains)

CATH v4.4 (24 domains)

7. Citations (1)

Structure of the YicI thiosugar Michaelis complex

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

2f2h__assembly_1__model_1

2f2h__assembly_1__model_1 | I(q)

2f2h__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 54 domains

SCOP 2.08 (30 domains)

CATH v4.4 (24 domains)

7. Citations (1)