SAXSdb — 9x3m

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

Xylan 1,4-beta-xylosidase

Pseudopedobacter saltans DSM 12145

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 × 8 D-xylose × 4 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	CALCIUM ION × 8 D-xylose × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	F0S5E9_PSESL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–432； UniProt 24–455 Author chain B； PDBConstruct 1–432； UniProt 24–455 Author chain C； PDBConstruct 1–432； UniProt 24–455 Author chain D； PDBConstruct 1–432； UniProt 24–455 Author chain E； PDBConstruct 1–432； UniProt 24–455 Author chain F； PDBConstruct 1–432； UniProt 24–455 Author chain G； PDBConstruct 1–432； UniProt 24–455 Author chain H； PDBConstruct 1–432； UniProt 24–455

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	9x3m
Deposition date deposition_date	2025-10-09
Last revision last_revision	2026-01-07
Structure title title	Crystal structure of Pseudopedobacter saltans GH43 beta-xylosidase in complex with xylose.
Keywords keywords	beta-xylosidase, 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.

9x3m__assembly_2__model_1

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

Download this curve (.dat)

9x3m__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9x3m__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	36.53 Å
Rg (electron density)	35.78 Å
Total Rg	36.42 Å
Atom count	13744
Residues	1728
Excluded volume	244270 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9x3m__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9x3m__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 (4)

Entity 1 Entity 1 polymer

Description description	Xylan 1,4-beta-xylosidase
Molecular weight formula_weight	48510.5 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	27742

QNPIIQTMYTADPAPMVYNNRLYVYTTHDEDQSTWFNMNDWKVYSTNDMVNWTDHGTILKYSDFAWAKGDAWAAQCVEKNGKFYLYVPVVSKVNNKGAIGVAVGDSPLGPFYDVLGKPLVQSEWGDIDPTVFIDDDGQAHMYWGNPKLKYVKLNEDMISYSGDIIEVPMTEESFGKRDGNPERPTKYEEGPWLYKRKDLYYLFWPGGPLPEFIGYSTSKSAKGPWKYGGIVMPAEGKSFTNHPGVIDFRGKTYFFYHNGALPGGSGFTRSVCVQELNFNKDGTIPQMKMTEGITKGIAALNPYQLTQAETISWSEHVKAFQNDKVGVFVRALQNGAYTSVKNVDFGDIGASAFSARVGTTHNGGVTMEIRMGSQEGPIAGTVKVPLTGGDDRWEIINVKLDRKITGIQDVYFVFKGKASSNIMYFDYWKFSK

Source Source

Source organism organism	Pseudopedobacter saltans DSM 12145
NCBI taxonomy ID ncbi_taxonomy_id	762903
Host organism host_organism	Escherichia coli BL21

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	16

Entity 3 Entity 3 non-polymer

Description description	D-xylose
Molecular weight formula_weight	150.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	244

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Unit-cell length a length_a	73.585 Å
Unit-cell length b length_b	89.435 Å
Unit-cell length c length_c	138.443 Å
Unit-cell angle α angle_alpha	102.82 °
Unit-cell angle β angle_beta	94.02 °
Unit-cell angle γ angle_gamma	97.88 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	47.841 Å
R factor r_factor	—
R_work r_work	0.2183
R_free r_free	0.2728

Crystal structure of Pseudopedobacter saltans GH43 beta-xylosidase in complex with xylose.

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

Xylan 1,4-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

9x3m__assembly_2__model_1

9x3m__assembly_2__model_1 | I(q)

9x3m__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 (4)

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 water

7. Citations (1)

Crystal structure of Pseudopedobacter saltans GH43 beta-xylosidase in complex with xylose.

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

Xylan 1,4-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

9x3m__assembly_2__model_1

9x3m__assembly_2__model_1 | I(q)

9x3m__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 (4)

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 water

7. Citations (1)