3c2u

Structure of the two subsite D-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane

Method: X-RAY DIFFRACTION

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

Xylosidase/arabinosidase

Selenomonas ruminantium

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O52575_SELRU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–538； UniProt 1–538 Author chain B； PDBConstruct 1–538； UniProt 1–538 Author chain C； PDBConstruct 1–538； UniProt 1–538 Author chain D； PDBConstruct 1–538； UniProt 1–538

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	3c2u
Deposition date deposition_date	2008-01-25
Structure title title	Structure of the two subsite D-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane
Keywords keywords	Tetramer; Glycoside Hydrolase; GH43; alpha-L-Arabinofuranosidase, 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.

3c2u__assembly_2__model_1

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

Download this curve (.dat)

3c2u__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c2u__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	31.74 Å
Rg (electron density)	30.87 Å
Total Rg	31.58 Å
Atom count	8698
Residues	1075
Excluded volume	153610 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c2u__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3c2u__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3c2u__assembly_3__model_1`	dimeric （2）	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	Xylosidase/arabinosidase
Molecular weight formula_weight	61200.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	19963

MNIQNPVLKGFNPDPSIVRAGDDYYIATSTFEWFPGVQIHHSKDLVHWHLVAHPLSTTEFLDMKGNPDSGGIWAPDLSYADGKFWLIYTDVKVVDGMWKDCHNYLTTAEDIKGPWSKPILLNGAGFDASLFHDPSGKKYLVNMYWDQRVYHHNFYGIALQEYSVAEEKLIGKPEIIYKGTDIAYTEGPHLYYINDMYYLMTAEGGTTYQHSETIARSKTIHGPYEIQPDYPLLSAWKEVHNPLQKCGHASLVETQNGQWYLAHLTGRPLPAPAGFPSREREQHAFCPLGRETAIQKIEWQDGWPVVVGGQQGSLEVEAPDLPQQEWAPTYEERDDFDKDTLNINFQTLRIPFSEHLGSLTARPGFLRLYGRESLQSKFTQAHIARRWQSFNFDAGTSVEFSPNSFQQMAGLTCYYNTENWSSIHVTWNEEKGRIIDLVTADNGTFSMPLAGAEIPIPDEVKTVHFKVSVRGRIYQYAYSFDGETFHTLPIELPSWKLSDDYVRGGGFFTGAFVGINAIDITGTALPADFDYFTYKELD

Source Source

Source organism organism	Selenomonas ruminantium
NCBI taxonomy ID ncbi_taxonomy_id	971
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	282.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2049

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3c2ua1
Class class	b — All beta proteins
Fold Fold fold	b.67 — 5-bladed beta-propeller
Superfamily Superfamily superfamily	b.67.2 — Arabinanase/levansucrase/invertase
Family Family family	b.67.2.0 — automated matches

Domain ID domain_id	d3c2ua2
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.29.1.0 — automated matches

Domain ID domain_id	d3c2ub1
Class class	b — All beta proteins
Fold Fold fold	b.67 — 5-bladed beta-propeller
Superfamily Superfamily superfamily	b.67.2 — Arabinanase/levansucrase/invertase
Family Family family	b.67.2.0 — automated matches

Domain ID domain_id	d3c2ub2
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.29.1.0 — automated matches

Domain ID domain_id	d3c2uc1
Class class	b — All beta proteins
Fold Fold fold	b.67 — 5-bladed beta-propeller
Superfamily Superfamily superfamily	b.67.2 — Arabinanase/levansucrase/invertase
Family Family family	b.67.2.0 — automated matches

Domain ID domain_id	d3c2uc2
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.29.1.0 — automated matches

Domain ID domain_id	d3c2ud1
Class class	b — All beta proteins
Fold Fold fold	b.67 — 5-bladed beta-propeller
Superfamily Superfamily superfamily	b.67.2 — Arabinanase/levansucrase/invertase
Family Family family	b.67.2.0 — automated matches

Domain ID domain_id	d3c2ud2
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.29.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	3c2uA01
Class class	2 — Mainly Beta
Architecture architecture	115 — 5 Propeller
Topology topology	10 — Tachylectin-2; Chain A
Homologous superfamily homologous superfamily	20 — Glycosyl hydrolase domain; family 43

Domain ID domain_id	3c2uA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3c2uB01
Class class	2 — Mainly Beta
Architecture architecture	115 — 5 Propeller
Topology topology	10 — Tachylectin-2; Chain A
Homologous superfamily homologous superfamily	20 — Glycosyl hydrolase domain; family 43

Domain ID domain_id	3c2uB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3c2uC01
Class class	2 — Mainly Beta
Architecture architecture	115 — 5 Propeller
Topology topology	10 — Tachylectin-2; Chain A
Homologous superfamily homologous superfamily	20 — Glycosyl hydrolase domain; family 43

Domain ID domain_id	3c2uC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3c2uD01
Class class	2 — Mainly Beta
Architecture architecture	115 — 5 Propeller
Topology topology	10 — Tachylectin-2; Chain A
Homologous superfamily homologous superfamily	20 — Glycosyl hydrolase domain; family 43

Domain ID domain_id	3c2uD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

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Unit-cell length a length_a	77.579 Å
Unit-cell length b length_b	84.401 Å
Unit-cell length c length_c	94.039 Å
Unit-cell angle α angle_alpha	67.84 °
Unit-cell angle β angle_beta	81.31 °
Unit-cell angle γ angle_gamma	75.08 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	87.040 Å
R factor r_factor	0.1357
R_work r_work	0.1343
R_free r_free	0.1630

Structure of the two subsite D-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane

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

Xylosidase/arabinosidase

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

3c2u__assembly_2__model_1

3c2u__assembly_2__model_1 | I(q)

3c2u__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structure of the two subsite D-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane

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

Xylosidase/arabinosidase

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

3c2u__assembly_2__model_1

3c2u__assembly_2__model_1 | I(q)

3c2u__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)