2bs9

Native crystal structure of a GH39 beta-xylosidase XynB1 from Geobacillus stearothermophilus

Method: X-RAY DIFFRACTION

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

BETA-XYLOSIDASE

BACILLUS STEAROTHERMOPHILUS

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 × 3 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	CALCIUM ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XYNB_GEOSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–503； UniProt 1–504 Author chain B； PDBConstruct 1–503； UniProt 1–504 Author chain C； PDBConstruct 1–503； UniProt 1–504 Author chain D； PDBConstruct 1–503； UniProt 1–504 Author chain E； PDBConstruct 1–503； UniProt 1–504 Author chain F； PDBConstruct 1–503； UniProt 1–504 Author chain G； PDBConstruct 1–503； UniProt 1–504 Author chain H； PDBConstruct 1–503； UniProt 1–504

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	2bs9
Deposition date deposition_date	2005-05-19
Structure title title	Native crystal structure of a GH39 beta-xylosidase XynB1 from Geobacillus stearothermophilus
Keywords keywords	HYDROLASE, BETA-XYLOSIDASE, COMPLEX OF THE COVALENT INTERMEDIATE, ENZYME-SUBSTRATE COMPLEX, FAMILY GH39, THERMOPHILIC ENZYME; 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.

2bs9__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2bs9__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2bs9__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	38.79 Å
Rg (electron density)	37.60 Å
Total Rg	38.23 Å
Atom count	16368
Residues	2004
Excluded volume	291670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2bs9__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2bs9__assembly_2__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	58058.8 kDa
EC 编号 ec_number	3.2.1.37
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	34099

MGVVNVPSNGREKFKKNWKFCVGTGRLGLALQKEYLDHLKLVQEKIGFRYIRGHGLLSDDVGIYREVEIDGEMKPFYNFTYIDRIVDSYLALNIRPFIEFGFMPKALASGDQTVFYWKGNVTPPKDYNKWRDLIVAVVSHFIERYGIEEVRTWLFEVWNEPNLVNFWKDANKQEYFKLYEVTARAVKSVDPHLQVGGPAICGGSDEWITDFLHFCAERRVPVDFVSRHAYTSKAPHKKTFEYYYQELEPPEDMLEQFKTVRALIRQSPFPHLPLHITEYNTSYSPINPVHDTALNAAYIARILSEGGDYVDSFSYWTFSDVFEEMDVPKALFHGGFGLVALHSIPKPTFHAFTFFNALGDELLYRDGEMIVTRRKDGSIAAVLWNLVMEKGEGLTKEVQLVIPVSESAVFIKRQIVNEQYGNAWRVWKQMGRPRFPSRQAVETLRQVAQPHVMTEQRRATDGVIHLSIVLSKNEVTLIEIEQVRDETSTYVGLDDGEITSYSS

Source Source

Source organism organism	BACILLUS STEAROTHERMOPHILUS
NCBI taxonomy ID ncbi_taxonomy_id	1422
Host organism host_organism	ESCHERICHIA COLI

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	7

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1367

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d2bs9a1
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	d2bs9a2
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	d2bs9b1
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	d2bs9b2
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	d2bs9c1
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	d2bs9c2
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	d2bs9d1
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	d2bs9d2
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	d2bs9e1
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	d2bs9e2
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	d2bs9f1
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	d2bs9f2
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	d2bs9g1
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	d2bs9g2
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	d2bs9h1
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	d2bs9h2
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 (16 domains)

Domain ID domain_id	2bs9A01
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	2bs9A02
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	2bs9B01
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	2bs9B02
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	2bs9C01
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	2bs9C02
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	2bs9D01
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	2bs9D02
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	2bs9E01
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	2bs9E02
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	2bs9F01
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	2bs9F02
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	2bs9G01
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	2bs9G02
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	2bs9H01
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	2bs9H02
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	92.668 Å
Unit-cell length b length_b	165.744 Å
Unit-cell length c length_c	311.004 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2110
R_work r_work	0.2090
R_free r_free	0.2590

Native crystal structure of a GH39 beta-xylosidase XynB1 from Geobacillus stearothermophilus

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

2bs9__assembly_2__model_1

2bs9__assembly_2__model_1 | I(q)

2bs9__assembly_2__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) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (2)

Native crystal structure of a GH39 beta-xylosidase XynB1 from Geobacillus stearothermophilus

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

2bs9__assembly_2__model_1

2bs9__assembly_2__model_1 | I(q)

2bs9__assembly_2__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) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (2)