SAXSdb — 3v90

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

Glycogenin-1

Oryctolagus cuniculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 4 CHLORIDE ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	GLYCEROL × 8 CHLORIDE ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLYG_RABIT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–291； UniProt 1–271

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	3v90
Deposition date deposition_date	2011-12-23
Structure title title	Structure of T82M glycogenin mutant truncated at residue 270
Keywords keywords	Transferase; 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.

3v90__assembly_1__model_1

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

Download this curve (.dat)

3v90__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3v90__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.54 Å
Rg (electron density)	25.73 Å
Total Rg	26.65 Å
Atom count	4154
Residues	520
Excluded volume	74254 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3v90__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3v90__assembly_2__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	Glycogenin-1
Molecular weight formula_weight	32637.8 kDa
EC 编号 ec_number	2.4.1.186
Mutation mutation	T82M
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	2190

MGSSHHHHHHSSGLVPRGSHMTDQAFVTLTTNDAYAKGALVLGSSLKQHRTSRRLAVLTTPQVSDTMRKALEIVFDEVITVDILDSGDSAHLTLMKRPELGVMLTKLHCWSLTQYSKCVFMDADTLVLANIDDLFEREELSAAPDPGWPDCFNSGVFVYQPSVETYNQLLHVASEQGSFDGGDQGLLNTFFNSWATTDIRKHLPFIYNLSSISIYSYLPAFKAFGANAKVVHFLGQTKPWNYTYDTKTKSVRSEGHDPTMTHPQFLNVWWDIFTTSVVPLLQQFGLVQDTC

Source Source

Source organism organism	Oryctolagus cuniculus
Common name common_name	European rabbit,Japanese white rabbit,domestic rabbit,rabbits
NCBI taxonomy ID ncbi_taxonomy_id	9986
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

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

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	113

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3v90a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
Superfamily Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
Family Family family	c.68.1.14 — Glycogenin

CATH v4.4 (1 domains)

Domain ID domain_id	3v90A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

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Unit-cell length a length_a	58.590 Å
Unit-cell length b length_b	102.790 Å
Unit-cell length c length_c	119.000 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	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	25.750 Å
R factor r_factor	0.1950
R_work r_work	0.1935
R_free r_free	0.2238

Structure of T82M glycogenin mutant truncated at residue 270

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

Glycogenin-1

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

3v90__assembly_1__model_1

3v90__assembly_1__model_1 | I(q)

3v90__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Structure of T82M glycogenin mutant truncated at residue 270

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

Glycogenin-1

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

3v90__assembly_1__model_1

3v90__assembly_1__model_1 | I(q)

3v90__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)