SAXSdb — 2yfr

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

LEVANSUCRASE

LACTOBACILLUS JOHNSONII

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 CHLORIDE ION × 1 ACETATE ION × 3 SULFATE ION × 9 GLYCEROL × 9 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 2 CHLORIDE ION × 2 ACETATE ION × 6 SULFATE ION × 18 GLYCEROL × 18 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q74K42_LACJO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–565； UniProt 145–708

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	2yfr
Deposition date deposition_date	2011-04-07
Structure title title	Crystal structure of inulosucrase from Lactobacillus johnsonii NCC533
Keywords keywords	FRUCTOSYLTRANSFERASE, GLYCOSIDE HYDROLASE FAMILY GH68, TRANSFERASE, SUGAR UTILIZATION; TRANSFERASE
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.

2yfr__assembly_2__model_1

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

Download this curve (.dat)

2yfr__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yfr__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	31.34 Å
Rg (electron density)	30.47 Å
Total Rg	31.21 Å
Atom count	8620
Residues	1068
Excluded volume	151190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yfr__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2yfr__assembly_2__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 (7)

Entity 1 Entity 1 polymer

Description description	LEVANSUCRASE
Molecular weight formula_weight	63853.4 kDa
EC 编号 ec_number	2.4.1.9
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	4909

MDVKQVEKKDSVDKTNAEENKDSSVKPAENATKAELKGQVKDIVEESGVDTSKLTNDQINELNKINFSKEAKSGTQLTYNDFKKIAKTLIEQDARYAIPFFNASKIKNMPAAKTLDAQSGKVEDLEIWDSWPVQDAKTGYVSNWNGYQLVIGMMGVPNVNDNHIYLLYNKYGDNDFNHWKNAGPIFGLGTPVIQQWSGSATLNKDGSIQLYYTKVDTSDNNTNHQKLASATVYLNLEKDQDKISIAHVDNDHIVFEGDGYHYQTYDQWKETNKGADNIAMRDAHVIDDDNGNRYLVFEASTGTENYQGDDQIYQWLNYGGTNKDNLGDFFQILSNSDIKDRAKWSNAAIGIIKLNDDVKNPSVAKVYSPLISAPMVSDEIERPDVVKLGNKYYLFAATRLNRGSNDDAWMATNKAVGDNVAMIGYVSDNLTHGYVPLNESGVVLTASVPANWRTATYSYYAVPVEGRDDQLLITSYITNRGEVAGKGMHATWAPSFLLQINPDNTTTVLAKMTNQGDWIWDDSSENPDMMGVLEKDAPNSAALPGEWGKPVDWDLIGGYNLKPHQHHHHHH

Source Source

Source organism organism	LACTOBACILLUS JOHNSONII
NCBI taxonomy ID ncbi_taxonomy_id	33959
Host organism host_organism	ESCHERICHIA COLI

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	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	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	9

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	9

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	515

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2yfrA01
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

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Unit-cell length a length_a	172.007 Å
Unit-cell length b length_b	172.007 Å
Unit-cell length c length_c	114.581 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	16

Space group space_group	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	121.630 Å
R factor r_factor	0.1519
R_work r_work	0.1510
R_free r_free	0.1696

Crystal structure of inulosucrase from Lactobacillus johnsonii NCC533

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

LEVANSUCRASE

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

2yfr__assembly_2__model_1

2yfr__assembly_2__model_1 | I(q)

2yfr__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 (7)

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 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of inulosucrase from Lactobacillus johnsonii NCC533

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

LEVANSUCRASE

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

2yfr__assembly_2__model_1

2yfr__assembly_2__model_1 | I(q)

2yfr__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 (7)

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 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)