1uhv

Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase

Method: X-RAY DIFFRACTION

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

Beta-xylosidase

Thermoanaerobacterium saccharolyticum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	1,5-anhydro-2-deoxy-2-fluoro-D-xylitol × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XYNB_THESA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–500； UniProt 1–500 Author chain B； PDBConstruct 1–500； UniProt 1–500 Author chain C； PDBConstruct 1–500； UniProt 1–500 Author chain D； PDBConstruct 1–500； UniProt 1–500

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	1uhv
Deposition date deposition_date	2003-07-11
Structure title title	Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase
Keywords keywords	family 39 glycoside hydrolase, xylosidase, xylan, xylose, covalent glycosyl-enzyme intermediate, 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.

1uhv__assembly_1__model_1

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

Download this curve (.dat)

1uhv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1uhv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.10 Å
Rg (electron density)	37.96 Å
Total Rg	38.54 Å
Atom count	16648
Residues	2000
Excluded volume	296180 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1uhv__assembly_1__model_1`	tetrameric （4）	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 (3)

Entity 1 Entity 1 polymer

Description description	Beta-xylosidase
Molecular weight formula_weight	58739.2 kDa
EC 编号 ec_number	3.2.1.37
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	17868

MIKVRVPDFSDKKFSDRWRYCVGTGRLGLALQKEYIETLKYVKENIDFKYIRGHGLLCDDVGIYREDVVGDEVKPFYNFTYIDRIFDSFLEIGIRPFVEIGFMPKKLASGTQTVFYWEGNVTPPKDYEKWSDLVKAVLHHFISRYGIEEVLKWPFEIWNEPNLKEFWKDADEKEYFKLYKVTAKAIKEVNENLKVGGPAICGGADYWIEDFLNFCYEENVPVDFVSRHAYTSKQGEYTPHLIYQEIMPSEYMLNEFKTVREIIKNSHFPNLPFHITEYNTSYSPQNPVHDTPFNAAYIARILSEGGDYVDSFSYWTFSDVFEERDVPRSQFHGGFGLVALNMIPKPTFYTFKFFNAMGEEMLYRDEHMLVTRRDDGSVALIAWNEVMDKTENPDEDYEVEIPVRFRDVFIKRQLIDEEHGNPWGTWIHMGRPRYPSKEQVNTLREVAKPEIMTSQPVANDGYLNLKFKLGKNAVVLYELTERIDESSTYIGLDDSKINGY

Source Source

Source organism organism	Thermoanaerobacterium saccharolyticum
NCBI taxonomy ID ncbi_taxonomy_id	28896
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,5-anhydro-2-deoxy-2-fluoro-D-xylitol
Molecular weight formula_weight	136.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1220

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1uhva1
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.71.1.2 — Composite domain of glycosyl hydrolase families 5, 30, 39 and 51

Domain ID domain_id	d1uhva2
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.1.8.3 — beta-glycanases

Domain ID domain_id	d1uhvb1
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.71.1.2 — Composite domain of glycosyl hydrolase families 5, 30, 39 and 51

Domain ID domain_id	d1uhvb2
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.1.8.3 — beta-glycanases

Domain ID domain_id	d1uhvc1
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.71.1.2 — Composite domain of glycosyl hydrolase families 5, 30, 39 and 51

Domain ID domain_id	d1uhvc2
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.1.8.3 — beta-glycanases

Domain ID domain_id	d1uhvd1
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.71.1.2 — Composite domain of glycosyl hydrolase families 5, 30, 39 and 51

Domain ID domain_id	d1uhvd2
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.1.8.3 — beta-glycanases

CATH v4.4 (8 domains)

Domain ID domain_id	1uhvA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1500 — Glycosyl hydrolase domain; family 39

Domain ID domain_id	1uhvA02
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	1uhvB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1500 — Glycosyl hydrolase domain; family 39

Domain ID domain_id	1uhvB02
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	1uhvC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1500 — Glycosyl hydrolase domain; family 39

Domain ID domain_id	1uhvC02
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	1uhvD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1500 — Glycosyl hydrolase domain; family 39

Domain ID domain_id	1uhvD02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

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Unit-cell length a length_a	95.326 Å
Unit-cell length b length_b	152.276 Å
Unit-cell length c length_c	159.684 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	32.330 Å
R factor r_factor	0.2100
R_work r_work	0.2100
R_free r_free	0.2620

Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase

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

Beta-xylosidase

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

1uhv__assembly_1__model_1

1uhv__assembly_1__model_1 | I(q)

1uhv__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase

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

Beta-xylosidase

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

1uhv__assembly_1__model_1

1uhv__assembly_1__model_1 | I(q)

1uhv__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)