SAXSdb — 1ups

▼

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

GLCNAC-ALPHA-1,4-GAL-RELEASING ENDO-BETA-GALACTOSIDASE

CLOSTRIDIUM PERFRINGENS

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 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q934G8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–420； UniProt 1–420 Author chain B； PDBConstruct 1–420； UniProt 1–420

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ups
Deposition date deposition_date	2003-10-10
Structure title title	GlcNAc[alpha]1-4Gal releasing endo-[beta]-galactosidase from Clostridium perfringens
Keywords keywords	;ENDO-GALACTOSIDASE, CLOSTRIDIUM PERFRINGENS, GLYCOSYL HYDROLASE, PSI, PROTEIN STRUCTURE INITIATIVE, SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS, SECSG ;; GLYCOSYL HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1ups__assembly_2__model_1

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

Download this curve (.dat)

1ups__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ups__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	25.72 Å
Rg (electron density)	24.82 Å
Total Rg	25.57 Å
Atom count	3268
Residues	397
Excluded volume	57096 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ups__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ups__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	GLCNAC-ALPHA-1,4-GAL-RELEASING ENDO-BETA-GALACTOSIDASE
Molecular weight formula_weight	49428.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6991

MFVFMLLLLLPFTISKAKDFPANPIEKAGYKLDFSDEFNGPTLDREKWTDYYLPHWCKDPESAKANYRFENGSLVEYITEDQKPWCPEHDGTVRSSAIMSFDKSWIHNFSGTTDNHERNEWRGYTTKYGYFEIRAKLSNTGGGGHQAWWMVGMQDDTNDWFNSKQTGEIDILETFFSKKDTWRIAAYGWNDPNFQTSWTISEDKVPSGDPTSEYHIYAMEWTPTALKFYYDNELFKVIYGSPDYEMGTILNIYTDAGSGAHNDVWPKEWAIDYMRVWKPVDGYKESESLNNYLIRNRQTGKFLYIEENNDKVSYGDITLKNEKNAKWSKEYRDGYTLLKNNETGEYLNIENQTGYIEHGKVPKTWWSAQWSEVPVDGYTRFVNRWKPNMSIHTESYEGVLQYGNVPNTYWTSQWQLIPVE

Source Source

Source organism organism	CLOSTRIDIUM PERFRINGENS
NCBI taxonomy ID ncbi_taxonomy_id	1502
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	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	378

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1upsa1
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.29.1.2 — Glycosyl hydrolases family 16

Domain ID domain_id	d1upsa2
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.3 — GlcNAc-alpha-1,4-Gal-releasing endo-beta-galactosidase, GngC, C-terminal domain

Domain ID domain_id	d1upsb1
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.29.1.2 — Glycosyl hydrolases family 16

Domain ID domain_id	d1upsb2
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.3 — GlcNAc-alpha-1,4-Gal-releasing endo-beta-galactosidase, GngC, C-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id	1upsA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1upsA02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1upsB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1upsB02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

▶

Unit-cell length a length_a	160.430 Å
Unit-cell length b length_b	160.430 Å
Unit-cell length c length_c	86.140 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
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	1.820 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1770
R_work r_work	0.1760
R_free r_free	0.2040

GlcNAc[alpha]1-4Gal releasing endo-[beta]-galactosidase from Clostridium perfringens

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

GLCNAC-ALPHA-1,4-GAL-RELEASING ENDO-BETA-GALACTOSIDASE

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

1ups__assembly_2__model_1

1ups__assembly_2__model_1 | I(q)

1ups__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

GlcNAc[alpha]1-4Gal releasing endo-[beta]-galactosidase from Clostridium perfringens

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

GLCNAC-ALPHA-1,4-GAL-RELEASING ENDO-BETA-GALACTOSIDASE

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

1ups__assembly_2__model_1

1ups__assembly_2__model_1 | I(q)

1ups__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)