1yi7

Beta-d-xylosidase (selenomethionine) XYND from Clostridium Acetobutylicum

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 × 7 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 4 GLYCEROL × 20 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 4–534； UniProt 2–532 Author chain B； PDBConstruct 4–534； UniProt 2–532 Author chain C； PDBConstruct 4–534； UniProt 2–532 Author chain D； PDBConstruct 4–534； UniProt 2–532

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	1yi7
Deposition date deposition_date	2005-01-11
Structure title title	Beta-d-xylosidase (selenomethionine) XYND from Clostridium Acetobutylicum
Keywords keywords	;Beta-propeller, beta-sandwich, Structural Genomics, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, 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.

1yi7__assembly_1__model_1

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

Download this curve (.dat)

1yi7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yi7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.12 Å
Rg (electron density)	38.41 Å
Total Rg	38.83 Å
Atom count	17583
Residues	2120
Excluded volume	310910 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yi7__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 (6)

Entity 1 Entity 1 polymer

Description description	Beta-xylosidase, family 43 glycosyl hydrolase
Molecular weight formula_weight	62655.1 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	20181

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	7

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	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	20

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2586

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d1yi7a1
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	d1yi7a2
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	d1yi7a3
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	d1yi7a4
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	d1yi7b1
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	d1yi7b2
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	d1yi7b3
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	d1yi7b4
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	d1yi7c1
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	d1yi7c2
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	d1yi7c3
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	d1yi7c4
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	d1yi7d1
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	d1yi7d2
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	d1yi7d3
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	d1yi7d4
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	1yi7A01
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	1yi7A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1yi7B01
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	1yi7B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1yi7C01
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	1yi7C02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1yi7D01
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	1yi7D02
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	89.130 Å
Unit-cell length b length_b	143.730 Å
Unit-cell length c length_c	188.690 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	1.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1440
R_work r_work	0.1420
R_free r_free	0.2020

Beta-d-xylosidase (selenomethionine) XYND from Clostridium Acetobutylicum

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

1yi7__assembly_1__model_1

1yi7__assembly_1__model_1 | I(q)

1yi7__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) 24 domains

SCOP 2.08 (16 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Beta-d-xylosidase (selenomethionine) XYND from Clostridium Acetobutylicum

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

1yi7__assembly_1__model_1

1yi7__assembly_1__model_1 | I(q)

1yi7__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) 24 domains

SCOP 2.08 (16 domains)

CATH v4.4 (8 domains)

7. Citations (1)