SAXSdb — 3akg

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

Putative secreted alpha L-arabinofuranosidase II

Streptomyces avermitilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose × 1 CHLORIDE ION × 1 SODIUM ION × 1 alpha-L-arabinofuranose × 2 GLYCEROL × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q82P90_STRAW
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–455； UniProt 28–481

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	3akg
Deposition date deposition_date	2010-07-14
Structure title title	Crystal structure of exo-1,5-alpha-L-arabinofuranosidase complexed with alpha-1,5-L-arabinofuranobiose
Keywords keywords	FIVE-BLADED BETA PROPELLER, BETA-TREFOIL, 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.

3akg__assembly_1__model_1

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

Download this curve (.dat)

3akg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3akg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.90 Å
Rg (electron density)	24.12 Å
Total Rg	24.87 Å
Atom count	3571
Residues	447
Excluded volume	62719 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3akg__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 (7)

Entity 1 Entity 1 polymer

Description description	Putative secreted alpha L-arabinofuranosidase II
Molecular weight formula_weight	51937.3 kDa
EC 编号 ec_number	3.2.1.55
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4023

MTAPASPSVTFTNPLAEKRADPHIFKHTDGYYYFTATVPEYDRIVLRRATTLQGLATAPETTIWTKHASGVMGAHIWAPEIHFIDGKWYVYFAAGSTSDVWAIRMYVLESGAANPLTGSWTEKGQIATPVSSFSLDATTFVVNGVRHLAWAQRNPAEDNNTSLFIAKMANPWTISGTPTEISQPTLSWETVGYKVNEGPAVIQHGGKVFLTYSASATDANYCLGMLSASASADLLNAASWTKSSQPVFKTSEATGQYGPGHNSFTVSEDGKSDILVYHDRNYKDISGDPLNDPNRRTRLQKVYWNADGTPNFGIPVADGVTPVRFSSYNYPDRYIRHWDFRARIEANVTNLADSQFRVVTGLAGSGTISLESANYPGYYLRHKNYEVWVEKNDGSSAFKNDASFSRRAGLADSADGIAFESYNYPGRYLRHYENLLRIQPVSTALDRQDATFYAEKLAAALEHHHHHH

Source Source

Source organism organism	Streptomyces avermitilis
NCBI taxonomy ID ncbi_taxonomy_id	227882
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose
Molecular weight formula_weight	282.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	alpha-L-arabinofuranose
Molecular weight formula_weight	150.1 kDa
Source method src_method	man
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	452

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3akgA01
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	3akgA02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	41.052 Å
Unit-cell length b length_b	91.765 Å
Unit-cell length c length_c	135.053 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	40.420 Å
R factor r_factor	0.1888
R_work r_work	0.1871
R_free r_free	0.2205

Crystal structure of exo-1,5-alpha-L-arabinofuranosidase complexed with alpha-1,5-L-arabinofuranobiose

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

Putative secreted alpha L-arabinofuranosidase II

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

3akg__assembly_1__model_1

3akg__assembly_1__model_1 | I(q)

3akg__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (3)

Crystal structure of exo-1,5-alpha-L-arabinofuranosidase complexed with alpha-1,5-L-arabinofuranobiose

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

Putative secreted alpha L-arabinofuranosidase II

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

3akg__assembly_1__model_1

3akg__assembly_1__model_1 | I(q)

3akg__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (3)