SAXSdb — 9glt

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

Ubiquitin-conjugating enzyme E2 13

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC13_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AAA； PDBConstruct 2–154； UniProt 1–153 Author chain BBB； PDBConstruct 2–154； UniProt 1–153

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	9glt
Deposition date deposition_date	2024-08-28
Last revision last_revision	2025-05-07
Structure title title	Crystal Structure of Yeast Ubc13 C87E
Keywords keywords	Ubiquitin conjugating protein E2 UBC13~UB thioester complex mimic, LIGASE; LIGASE
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.

9glt__assembly_1__model_1

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

Download this curve (.dat)

9glt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9glt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.28 Å
Rg (electron density)	16.01 Å
Total Rg	17.16 Å
Atom count	1188
Residues	149
Excluded volume	21281 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9glt__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9glt__assembly_2__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 (2)

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Unit-cell length a length_a	25.603 Å
Unit-cell length b length_b	127.663 Å
Unit-cell length c length_c	42.330 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.21 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	42.080 Å
R factor r_factor	—
R_work r_work	0.1913
R_free r_free	0.2280

Description description	Ubiquitin-conjugating enzyme E2 13
Molecular weight formula_weight	17573.0 kDa
EC 编号 ec_number	2.3.2.23
Mutation mutation	C87E
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	AAA,BBB
Atom count atom_count	2680

Crystal Structure of Yeast Ubc13 C87E

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

Ubiquitin-conjugating enzyme E2 13

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

9glt__assembly_1__model_1

9glt__assembly_1__model_1 | I(q)

9glt__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

7. Citations (1)

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	292

Crystal Structure of Yeast Ubc13 C87E

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

Ubiquitin-conjugating enzyme E2 13

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

9glt__assembly_1__model_1

9glt__assembly_1__model_1 | I(q)

9glt__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

7. Citations (1)