2exk

Structure of the family43 beta-Xylosidase E187G from geobacillus stearothermophilus in complex with xylobiose

Method: X-RAY DIFFRACTION

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

beta-D-xylosidase

Geobacillus stearothermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 4 其他Polymer 4	alpha-D-xylopyranose-(1-4)-alpha-D-xylopyranose × 4 CALCIUM ION × 4 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 3 GLYCEROL × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q68HB3_BACST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–535； UniProt 1–535 Author chain B； PDBConstruct 1–535； UniProt 1–535 Author chain C； PDBConstruct 1–535； UniProt 1–535 Author chain D； PDBConstruct 1–535； UniProt 1–535

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	2exk
Deposition date deposition_date	2005-11-08
Structure title title	Structure of the family43 beta-Xylosidase E187G from geobacillus stearothermophilus in complex with xylobiose
Keywords keywords	glykosidase, hydrolsase, xylosidase, family43, xylose, 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.

2exk__assembly_1__model_1

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

Download this curve (.dat)

2exk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2exk__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)	38.28 Å
Total Rg	38.77 Å
Atom count	17624
Residues	2132
Excluded volume	311110 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2exk__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-D-xylosidase
Molecular weight formula_weight	61897.2 kDa
EC 编号 ec_number	3.2.1.37
Mutation mutation	E187G
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	18715

MAKIKNPILTGFHPDPSICRVGDDYYIAVSTFEWFPGVRIYHSKDLKNWRLVARPLNRLSQLNMIGNPDSGGVWAPHLSYSDGKFWLIYTDVKVVEGQWKDGHNYLVTCDTIDGAWSDPIYLNSSGFDPSLFHDEDGRKYLVNMYWDHRVDHHPFYGIVLQEYSVEQKKLVGEPKIIFKGTDLRITGGPHLYKINGYYYLLTAEGGTRYNHAATIARSTSLYGPYEVHPDNPLLTSWPYPRNPLQKAGHASIVHTHTDEWFLVHLTGRPLPREGQPLLEHRGYCPLGRETAIQRLEWKDGWPYVVGGNGPSLEIDGPSVEEVSWEKDYDEKDDFDGDTLNHHFQTLRIPLGEDIATLKARPGHLRLYGRESLTSRFTQAFVARRWQHFHFVAETKVSFRPTTFQQSAGLVNYYNTQNWTTLQITWHEEKGRILELMTCDHLVVDQPLRGREIVVPDDIEYVYLRVTVQATTYKYSYSFDGMNWIDLPVTFESYKLSDDYIKSRAAFTGAFVGMHCRDGSGQNNYADFDYFLYKEL

Source Source

Source organism organism	Geobacillus stearothermophilus
NCBI taxonomy ID ncbi_taxonomy_id	1422
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 branched

Description description	alpha-D-xylopyranose-(1-4)-alpha-D-xylopyranose
Molecular weight formula_weight	282.2 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	3

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	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1091

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2exka1
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	d2exka2
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	d2exkb1
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	d2exkb2
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	d2exkc1
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	d2exkc2
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	d2exkd1
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	d2exkd2
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

CATH v4.4 (8 domains)

Domain ID domain_id	2exkA01
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	2exkA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	2exkB01
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	2exkB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	2exkC01
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	2exkC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	2exkD01
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	2exkD02
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	139.870 Å
Unit-cell length b length_b	139.870 Å
Unit-cell length c length_c	232.025 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	32

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	2.230 Å
R factor r_factor	0.1880
R_work r_work	0.1850
R_free r_free	0.2380

Structure of the family43 beta-Xylosidase E187G from geobacillus stearothermophilus in complex with xylobiose

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

beta-D-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

2exk__assembly_1__model_1

2exk__assembly_1__model_1 | I(q)

2exk__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 branched

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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (3)

Structure of the family43 beta-Xylosidase E187G from geobacillus stearothermophilus in complex with xylobiose

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

beta-D-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

2exk__assembly_1__model_1

2exk__assembly_1__model_1 | I(q)

2exk__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 branched

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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (3)