SAXSdb — 2xvg

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

ALPHA XYLOSIDASE

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 4 1,2-ETHANEDIOL × 3 SULFATE ION × 1 NICKEL (II) ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B3PBD9_CELJU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–988； UniProt 1–988

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	2xvg
Deposition date deposition_date	2010-10-26
Structure title title	crystal structure of alpha-xylosidase (GH31) from Cellvibrio japonicus
Keywords keywords	HYDROLASE, GLYCOSYL HYDROLASE FAMILY 31, BETA/ALPHA 8 BARREL; 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.

2xvg__assembly_1__model_1

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

Download this curve (.dat)

2xvg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2xvg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.99 Å
Rg (electron density)	27.95 Å
Total Rg	28.93 Å
Atom count	7600
Residues	944
Excluded volume	134200 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2xvg__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 (6)

Entity 1 Entity 1 polymer

Description description	ALPHA XYLOSIDASE
Molecular weight formula_weight	115203.9 kDa
EC 编号 ec_number	3.2.1.-
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7703

MLSAHQWLRHCIIGVASVALLQACSKQTGNESSSSAKSATEQVKALAQVERTAEGVVLTLPEGTVKKLRLQVMGERIIRVTALPGTDFGIVPESIQVVAKPATNVPFSVDQAGEKLVLKTSQVSAEVSLLDGTVSFRDAKGNVLLQEENRGTFSPVIHDPDPVDADSYALRQEFNRGSDEGFFGLGQHQNGQVNYAGENVELTTYNLVISIPFLVSSRNYGLLWDNNSITRFGDPREAQPLNQSLKLYDAEGKEGGLTVRYFVGDELKLTRVEADFNHQFYKQGNELENPFPEEVAGAYKNNTLRIELEGSIEAQATGKHQFKMYNSGYAQLSLDGEVVLDRWRMNWNPWYHNFYRELNAGDKHKLKVSWKPDGGFFHLRHLDPLPANEQHELSLASETGKAIDYYFVAGDTKDDIISGYRQLTGKSVMLPKWAYGFWQSRERYKSSDEIIQNLKEYRDRKIPIDNIVLDWSYWPEDAWGSHDFDKQFFPDPKALVDKVHAMNAQIMISVWPKFYPTTDNYKELNAKGFMFNRNLDEKNLDWIGKGYLNAFYDPFSPEATAIFWKQIRDKINVHGFDAWWLDAVEPDIHSNLTFEKRKWLMTPNARGNGAEIFNAYAVPHAEGVYQGELATDGDKRSFILTRSGFGGIQRTGSAIWSGDIVSRWSDMKDQIAAGIGTNLAGVTNWTFDIGGFTPEDRFRHGKKGFVGSWTALDAEQVDEWQELNTRWYQFGAFVPLYRSHGQNPYREIFNIADEGTEVYNAMVWYTKLRYYLMPYIYTLGGDTYHKDGTIMRGLVMDFPNDRKAWDINTQYMFGPAFLVNPVYEYKARSRDVYLPAGSDWYNFYTGEKLAGGQTITADAPLARVPLFVKAGAIVPTGPLIQHVDEGLNSPLLITVYTGANGSFDIYEDDGRSLKYQQGEWSRIPLSYDDVTGTLIIGDRVGSFTGMADERNIRVRFIAGPTADATNFDKAAAEAVTYTGKSVSIKRPRKVVINSKLEGKPIPNPLLGLDSTRTGHHHHHH

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	103

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6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2xvga1
Class class	b — All beta proteins
Fold Fold fold	b.30 — Supersandwich
Superfamily Superfamily superfamily	b.30.5 — Galactose mutarotase-like
Family Family family	b.30.5.11 — Glycosyl hydrolase family 31, N-terminal domain-like

Domain ID domain_id	d2xvga2
Class class	b — All beta proteins
Fold Fold fold	b.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamily	b.179.1 — PA14-like
Family Family family	b.179.1.3 — Glycoside hydrolase family 31 (GH31), PA14-like domain

Domain ID domain_id	d2xvga3
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.1.8.13 — Glycosyl hydrolase family 31 catalytic domain

Domain ID domain_id	d2xvga4
Class class	b — All beta proteins
Fold Fold fold	b.71 — Glycosyl hydrolase domain
Superfamily Superfamily superfamily	b.71.1 — Glycosyl hydrolase domain
Family Family family	b.71.1.4 — Glycosyl hydrolase family 31, domain 3

Domain ID domain_id	d2xvga5
Class class	b — All beta proteins
Fold Fold fold	b.150 — Glycolsyl hydrolase family 31 C-terminal domain-like
Superfamily Superfamily superfamily	b.150.1 — Glycolsyl hydrolase family 31 C-terminal domain
Family Family family	b.150.1.1 — Glycolsyl hydrolase family 31 C-terminal domain

Domain ID domain_id	d2xvga6
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (5 domains)

Domain ID domain_id	2xvgA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1760 — glycosyl hydrolase (family 31)

Domain ID domain_id	2xvgA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	380 —

Domain ID domain_id	2xvgA03
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	2xvgA04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	2xvgA05
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

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Unit-cell length a length_a	156.193 Å
Unit-cell length b length_b	156.193 Å
Unit-cell length c length_c	227.759 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	49.885 Å
R factor r_factor	0.2065
R_work r_work	0.2038
R_free r_free	0.2590

crystal structure of alpha-xylosidase (GH31) from Cellvibrio japonicus

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

ALPHA 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

2xvg__assembly_1__model_1

2xvg__assembly_1__model_1 | I(q)

2xvg__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

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 water

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

CATH v4.4 (5 domains)

7. Citations (1)

crystal structure of alpha-xylosidase (GH31) from Cellvibrio japonicus

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

ALPHA 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

2xvg__assembly_1__model_1

2xvg__assembly_1__model_1 | I(q)

2xvg__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

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 water

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

CATH v4.4 (5 domains)

7. Citations (1)