9ywn

Protein Structure of the First Glycoside Hydrolase Family 30, Subfamily 12 Endoxylanase

Method: X-RAY DIFFRACTION

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

Glucuronoarabinoxylan endo-1,4-beta-xylanase

Anaerobacterium chartisolvens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	GLYCEROL × 4 FORMIC ACID × 1 ACETIC ACID × 2 1,2-ETHANEDIOL × 1 SODIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	GLYCEROL × 5 FORMIC ACID × 1 1,2-ETHANEDIOL × 4 SODIUM ION × 1 DI(HYDROXYETHYL)ETHER × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	GLYCEROL × 6 FORMIC ACID × 2 ACETIC ACID × 2 1,2-ETHANEDIOL × 1 SODIUM ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	GLYCEROL × 3 FORMIC ACID × 4 1,2-ETHANEDIOL × 1 SODIUM ION × 1 DI(HYDROXYETHYL)ETHER × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	GLYCEROL × 3 FORMIC ACID × 2 ACETIC ACID × 1 1,2-ETHANEDIOL × 1 SODIUM ION × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	GLYCEROL × 1 FORMIC ACID × 2 ACETIC ACID × 1 1,2-ETHANEDIOL × 4 SODIUM ION × 1 DI(HYDROXYETHYL)ETHER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A369AIV8_9FIRM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 26–446； UniProt 30–450 Author chain B； PDBConstruct 26–446； UniProt 30–450 Author chain C； PDBConstruct 26–446； UniProt 30–450 Author chain D； PDBConstruct 26–446； UniProt 30–450 Author chain E； PDBConstruct 26–446； UniProt 30–450 Author chain F； PDBConstruct 26–446； UniProt 30–450

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	9ywn
Deposition date deposition_date	2025-10-24
Last revision last_revision	2026-04-15
Structure title title	Protein Structure of the First Glycoside Hydrolase Family 30, Subfamily 12 Endoxylanase
Keywords keywords	glycoside hydrolase, Xylanase, Endoxylanase, 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.

9ywn__assembly_1__model_1

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

Download this curve (.dat)

9ywn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ywn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.98 Å
Rg (electron density)	21.76 Å
Total Rg	22.72 Å
Atom count	3365
Residues	424
Excluded volume	59593 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ywn__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9ywn__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9ywn__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`9ywn__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`9ywn__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`9ywn__assembly_6__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 (8)

Entity 1 Entity 1 polymer

Description description	Glucuronoarabinoxylan endo-1,4-beta-xylanase
Molecular weight formula_weight	49706.9 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	22256

MHHHHHHSSGVDLGTENLYFQSNAMAYSVSVDINTSYQTLEGFGAAIAWSNESLTEHPNRAGLYKTLFFDSGLDILRLRNQYRNSSDFAYPDTEIVKLARCFNPNLKILLCSWTPPADIKENGVLNGGTLIKQNGAFVYDRFADYWYKSLNAYAAKGIVPDYISIQNEPDYQSSDWETCIFYPTETSNYPGYDKALDAVYSKLQTLPSMPKIIAAEATGIGTSMIGNNAAQQYFNKIDFSKIYGLAHHLYNGGDPNNPDSFNSVFKAIAAAYPGKPIFQTEYDQGTPFTTTQLIHNSLVEEGVSSYFFWDLIWDNSQRPMVIVEPPFNQNGWSNPQGYYKTDFYSSIQHYAKFTEPGYSRVKAESSGSNVSVTAFTSPGKDKLTLVLINKASSESTISLNLNGYTADTSAVYRTVFSGTAERFAHLGSLQGNTVTMPAQSVVTVALE

Source Source

Source organism organism	Anaerobacterium chartisolvens
NCBI taxonomy ID ncbi_taxonomy_id	1297424
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	22

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1630

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Unit-cell length a length_a	89.307 Å
Unit-cell length b length_b	133.392 Å
Unit-cell length c length_c	137.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.54 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.916 Å
Low-resolution limit resolution_low	48.949 Å
R factor r_factor	—
R_work r_work	0.1686
R_free r_free	0.2050

Protein Structure of the First Glycoside Hydrolase Family 30, Subfamily 12 Endoxylanase

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

Glucuronoarabinoxylan 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

9ywn__assembly_1__model_1

9ywn__assembly_1__model_1 | I(q)

9ywn__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 (8)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

Protein Structure of the First Glycoside Hydrolase Family 30, Subfamily 12 Endoxylanase

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

Glucuronoarabinoxylan 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

9ywn__assembly_1__model_1

9ywn__assembly_1__model_1 | I(q)

9ywn__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 (8)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)