SAXSdb — 2dcy

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

Endo-1,4-beta-xylanase A

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	1,4-DIETHYLENE DIOXIDE × 1 L(+)-TARTARIC ACID × 1 D(-)-TARTARIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	1,4-DIETHYLENE DIOXIDE × 1 L(+)-TARTARIC ACID × 3 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	1,4-DIETHYLENE DIOXIDE × 1 L(+)-TARTARIC ACID × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	L(+)-TARTARIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XYNA_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–185； UniProt 29–213 Author chain B； PDBConstruct 1–185； UniProt 29–213 Author chain C； PDBConstruct 1–185； UniProt 29–213 Author chain D； PDBConstruct 1–185； UniProt 29–213 Author chain E； PDBConstruct 1–185； UniProt 29–213

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	2dcy
Deposition date deposition_date	2006-01-18
Structure title title	Crystal structure of Bacillus subtilis family-11 xylanase
Keywords keywords	ALL BETA, 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.

2dcy__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2dcy__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dcy__assembly_5__model_1 | P(r) · Pending

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

Rg（Guinier）	16.43 Å
Rg (electron density)	15.05 Å
Total Rg	16.21 Å
Atom count	1457
Residues	185
Excluded volume	25216 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dcy__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2dcy__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2dcy__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2dcy__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2dcy__assembly_5__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 (5)

Entity 1 Entity 1 polymer

Description description	Endo-1,4-beta-xylanase A
Molecular weight formula_weight	20395.0 kDa
EC 编号 ec_number	3.2.1.8
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	7611

ASTDYWQNWTDGGGIVNAVNGSGGNYSVNWSNTGNFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDRTTFTQYWSVRQSKRPTGSNATITFSNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVW

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,4-DIETHYLENE DIOXIDE
Molecular weight formula_weight	88.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	L(+)-TARTARIC ACID
Molecular weight formula_weight	150.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	D(-)-TARTARIC ACID
Molecular weight formula_weight	150.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	248

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d2dcya_
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.29.1.11 — Xylanase/endoglucanase 11/12

Domain ID domain_id	d2dcyb_
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.29.1.11 — Xylanase/endoglucanase 11/12

Domain ID domain_id	d2dcyc_
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.29.1.11 — Xylanase/endoglucanase 11/12

Domain ID domain_id	d2dcyd_
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.29.1.11 — Xylanase/endoglucanase 11/12

Domain ID domain_id	d2dcye_
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.29.1.11 — Xylanase/endoglucanase 11/12

CATH v4.4 (5 domains)

Domain ID domain_id	2dcyA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	180 — Glycoside hydrolase family 11/12, catalytic domain

Domain ID domain_id	2dcyB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	180 — Glycoside hydrolase family 11/12, catalytic domain

Domain ID domain_id	2dcyC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	180 — Glycoside hydrolase family 11/12, catalytic domain

Domain ID domain_id	2dcyD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	180 — Glycoside hydrolase family 11/12, catalytic domain

Domain ID domain_id	2dcyE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	180 — Glycoside hydrolase family 11/12, catalytic domain

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Unit-cell length a length_a	130.445 Å
Unit-cell length b length_b	186.209 Å
Unit-cell length c length_c	37.979 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	20

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1983
R_work r_work	0.1973
R_free r_free	0.2173

Crystal structure of Bacillus subtilis family-11 xylanase

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

Endo-1,4-beta-xylanase A

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

2dcy__assembly_5__model_1

2dcy__assembly_5__model_1 | I(q)

2dcy__assembly_5__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Crystal structure of Bacillus subtilis family-11 xylanase

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

Endo-1,4-beta-xylanase A

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

2dcy__assembly_5__model_1

2dcy__assembly_5__model_1 | I(q)

2dcy__assembly_5__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)