SAXSdb — 3emq

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

Endo-1,4-beta-xylanase

Bacillus sp. BP-23

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(1S,2S,3R,6R)-6-[(2-hydroxybenzyl)amino]cyclohex-4-ene-1,2,3-triol × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O69231_9BACI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–331； UniProt 2–332

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	3emq
Deposition date deposition_date	2008-09-25
Structure title title	Crystal structure of xilanase XynB from Paenibacillus barcelonensis complexed with an inhibitor
Keywords keywords	(alpha/beta)8 barrel, 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.

3emq__assembly_1__model_1

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

Download this curve (.dat)

3emq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3emq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.89 Å
Rg (electron density)	19.62 Å
Total Rg	20.63 Å
Atom count	2733
Residues	331
Excluded volume	47978 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3emq__assembly_1__model_1`	monomeric （1）	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	Endo-1,4-beta-xylanase
Molecular weight formula_weight	38475.9 kDa
EC 编号 ec_number	3.2.1.8
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2998

STEIPSLSASYANSFKIGAAVHTRMLQTEGEFIAKHYNSVTAENQMKFEEVHPREHEYTFEAADEIVDFAVARGIGVRGHTLVWHNQTPAWMFEDASGGTASREMMLSRLKQHIDTVVGRYKDQIYAWDVVNEAIEDKTDLIMRDTKWLRLLGEDYLVQAFNMAHEADPNALLFYNDYNETDPVKREKIYNLVRSLLDQGAPVHGIGMQGHWNIHGPSMDEIRQAIERYASLDVQLHVTELDLSVFRHEDQRTDLTEPTAEMAELQQKRYEDIFGLFREYRSNITSVTFWGVADNYTWLDNFPVRGRKNWPFVFDTELQPKDSFWRIIGQD

Source Source

Source organism organism	Bacillus sp. BP-23
NCBI taxonomy ID ncbi_taxonomy_id	89769
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(1S,2S,3R,6R)-6-[(2-hydroxybenzyl)amino]cyclohex-4-ene-1,2,3-triol
Molecular weight formula_weight	251.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	265

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3emqa_
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 (1 domains)

Domain ID domain_id	3emqA00
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	44.390 Å
Unit-cell length b length_b	79.640 Å
Unit-cell length c length_c	93.420 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.730 Å
Low-resolution limit resolution_low	16.920 Å
R factor r_factor	—
R_work r_work	0.2080
R_free r_free	0.3060

Crystal structure of xilanase XynB from Paenibacillus barcelonensis complexed with an inhibitor

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

Endo-1,4-beta-xylanase

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

3emq__assembly_1__model_1

3emq__assembly_1__model_1 | I(q)

3emq__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of xilanase XynB from Paenibacillus barcelonensis complexed with an inhibitor

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

Endo-1,4-beta-xylanase

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

3emq__assembly_1__model_1

3emq__assembly_1__model_1 | I(q)

3emq__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)