1y7b

BETA-D-XYLOSIDASE, A FAMILY 43 GLYCOSIDE HYDROLASE

Method: X-RAY DIFFRACTION

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

Beta-xylosidase, family 43 glycosyl hydrolase

Clostridium acetobutylicum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	CALCIUM ION × 4 SULFATE ION × 6 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 4 TRIETHYLENE GLYCOL × 1 GLYCEROL × 14 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q97DM1_CLOAB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–535； UniProt 1–533 Author chain B； PDBConstruct 1–535； UniProt 1–533 Author chain C； PDBConstruct 1–535； UniProt 1–533 Author chain D； PDBConstruct 1–535； UniProt 1–533

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	1y7b
Deposition date deposition_date	2004-12-08
Structure title title	BETA-D-XYLOSIDASE, A FAMILY 43 GLYCOSIDE HYDROLASE
Keywords keywords	;beta-propeller, beta-sandwich, structural genomics, protein structure initative, PSI, New York SGX Research Center for Structural Genomics, NYSGXRC, Protein Structure Initiative, 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.

1y7b__assembly_1__model_1

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

Download this curve (.dat)

1y7b__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1y7b__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.27 Å
Rg (electron density)	38.51 Å
Total Rg	39.02 Å
Atom count	17552
Residues	2136
Excluded volume	310130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1y7b__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 (7)

Entity 1 Entity 1 polymer

Description description	Beta-xylosidase, family 43 glycosyl hydrolase
Molecular weight formula_weight	62420.6 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	20552

MSLIKNPILRGFNPDPSICRADTDYYIATSTFEWFPGVQIHHSKDLVNWHLVAHPLNRTSLLDMKGNPNSGGIWAPDLSYHDGKFWLIYTDVKVTDGMWKDCHNYLTTCESVDGVWSDPITLNGSGFDASLFHDNDGKKYLVNMYWDQRTYNHNFYGIVLQEYSDKEKKLIGKAKIIYKGTDIKYTEGPHIYHIGDYYYLFTAEGGTTYEHSETVARSKNIDGPYEIDPEYPLLTSWHDPRNSLQKCGHASLVHTHTDEWYLAHLVGRPLPVGNQPVLEQRGYCPLGRETSIQRIEWVDNWPRVVGGKQGSVNVEAPKIPEVKWEKTYDEKDNFDSDKLNINFQSLRIPLTENIASLKAKKGNLRLYGKESLTSTFTQAFIARRWQSFKFDASTSVSFSPDTFQQAAGLTCYYNTENWSTIQVTWNEDKGRVIDIVCCDNFHFDMPLKSNVIPIPKDVEYIHLKVEVRVETYQYSYSFDGINWSKVPAIFESRKLSDDYVQGGGFFTGAFVGINCIDITGNNKPADFDYFCYKEEGHHHHHH

Source Source

Source organism organism	Clostridium acetobutylicum
NCBI taxonomy ID ncbi_taxonomy_id	272562
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3000

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d1y7ba1
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.23 — Beta-D-xylosidase C-terminal domain-like

Domain ID domain_id	d1y7ba2
Class class	b — All beta proteins
Fold Fold fold	b.67 — 5-bladed beta-propeller
Superfamily Superfamily superfamily	b.67.2 — Arabinanase/levansucrase/invertase
Family Family family	b.67.2.1 — alpha-L-arabinanase-like

Domain ID domain_id	d1y7ba3
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	d1y7ba4
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	d1y7bb1
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.23 — Beta-D-xylosidase C-terminal domain-like

Domain ID domain_id	d1y7bb2
Class class	b — All beta proteins
Fold Fold fold	b.67 — 5-bladed beta-propeller
Superfamily Superfamily superfamily	b.67.2 — Arabinanase/levansucrase/invertase
Family Family family	b.67.2.1 — alpha-L-arabinanase-like

Domain ID domain_id	d1y7bb3
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	d1y7bb4
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	d1y7bc1
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.23 — Beta-D-xylosidase C-terminal domain-like

Domain ID domain_id	d1y7bc2
Class class	b — All beta proteins
Fold Fold fold	b.67 — 5-bladed beta-propeller
Superfamily Superfamily superfamily	b.67.2 — Arabinanase/levansucrase/invertase
Family Family family	b.67.2.1 — alpha-L-arabinanase-like

Domain ID domain_id	d1y7bc3
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	d1y7bc4
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	d1y7bd1
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.23 — Beta-D-xylosidase C-terminal domain-like

Domain ID domain_id	d1y7bd2
Class class	b — All beta proteins
Fold Fold fold	b.67 — 5-bladed beta-propeller
Superfamily Superfamily superfamily	b.67.2 — Arabinanase/levansucrase/invertase
Family Family family	b.67.2.1 — alpha-L-arabinanase-like

Domain ID domain_id	d1y7bd3
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	d1y7bd4
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 (8 domains)

Domain ID domain_id	1y7bA01
Class class	2 — Mainly Beta
Architecture architecture	115 — 5 Propeller
Topology topology	10 — Tachylectin-2; Chain A
Homologous superfamily homologous superfamily	20 — Glycosyl hydrolase domain; family 43

Domain ID domain_id	1y7bA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1y7bB01
Class class	2 — Mainly Beta
Architecture architecture	115 — 5 Propeller
Topology topology	10 — Tachylectin-2; Chain A
Homologous superfamily homologous superfamily	20 — Glycosyl hydrolase domain; family 43

Domain ID domain_id	1y7bB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1y7bC01
Class class	2 — Mainly Beta
Architecture architecture	115 — 5 Propeller
Topology topology	10 — Tachylectin-2; Chain A
Homologous superfamily homologous superfamily	20 — Glycosyl hydrolase domain; family 43

Domain ID domain_id	1y7bC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1y7bD01
Class class	2 — Mainly Beta
Architecture architecture	115 — 5 Propeller
Topology topology	10 — Tachylectin-2; Chain A
Homologous superfamily homologous superfamily	20 — Glycosyl hydrolase domain; family 43

Domain ID domain_id	1y7bD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

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Unit-cell length a length_a	94.480 Å
Unit-cell length b length_b	136.150 Å
Unit-cell length c length_c	183.870 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	1.600 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1580
R_work r_work	0.1570
R_free r_free	0.2060

BETA-D-XYLOSIDASE, A FAMILY 43 GLYCOSIDE HYDROLASE

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

Beta-xylosidase, family 43 glycosyl hydrolase

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

1y7b__assembly_1__model_1

1y7b__assembly_1__model_1 | I(q)

1y7b__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

CATH v4.4 (8 domains)

7. Citations (1)

BETA-D-XYLOSIDASE, A FAMILY 43 GLYCOSIDE HYDROLASE

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

Beta-xylosidase, family 43 glycosyl hydrolase

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

1y7b__assembly_1__model_1

1y7b__assembly_1__model_1 | I(q)

1y7b__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

CATH v4.4 (8 domains)

7. Citations (1)