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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain AAA； UniProt 1–153	Mutation：C87E	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M sodium cacodylate, pH 6.5, 25% PEG 4000	Resolution 1.45 Å R-free 0.228
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain BBB； UniProt 1–153	Mutation：C87E	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M sodium cacodylate, pH 6.5, 25% PEG 4000	Resolution 1.45 Å R-free 0.228

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9GLT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JAT Mms2/Ubc13 Ubiquitin Conjugating Enzyme Complex Deposited 2001-05-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–153（152 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 1000, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.239
1JBB Ubiquitin Conjugating Enzyme, Ubc13 Deposited 2001-06-03	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–153（153 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 5000-MME, ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.255
1JBB Ubiquitin Conjugating Enzyme, Ubc13 Deposited 2001-06-03	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–153（153 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 5000-MME, ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.255
2GMI Mms2/Ubc13~Ubiquitin Deposited 2006-04-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–152（152 aa）	Mutation：C87S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；17% PEG 1000, 100 mM Na/K phosphate, pH 6.2, 25 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.268
4FH1 S. cerevisiae Ubc13-N79A Deposited 2012-06-05	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–153（153 aa）	Mutation：N79A, C87S	NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.3；296 K；0.1 M CHES, pH 10.3, 20% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.61 Å R-free 0.246
5OJW S. cerevisiae UBC13 - MMs2 complex Deposited 2017-07-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–152（152 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；292 K；0.1M Bis-Tris Propane / Citric Acid Buffer, pH 7.6, 20% PEG3000	Resolution 2.00 Å R-free 0.205
6ZHS Uba1 bound to two E2 (Ubc13) molecules Deposited 2020-06-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–153（153 aa） Chain C 1–153（153 aa）	Not recorded	SO4 SULFATE ION × 2 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；273 K；ammonium sulfate, HEPES, PEG 3350	Resolution 2.35 Å R-free 0.275
6ZHT Uba1-Ubc13 disulfide mediated complex Deposited 2020-06-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–152（152 aa）	Not recorded	GOL GLYCEROL × 12 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；273 K；ammonium nitrate, CHES, PEG 4000	Resolution 2.30 Å R-free 0.263

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

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
最后修订 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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.39 Å
Radius of gyration Rg (electron density) rg_electron	23.94 Å
Forward intensity I(0) i0	17958200.00
Molecular weight molecular_weight	33404.0 kDa
Excluded volume excluded_volume	42350 Å³
Envelope volume envelope_volume	52378 Å³
Hydration-shell volume shell_volume	19498 Å³
Envelope diameter envelope_diameter	88.1 Å
Shell Rg shell_rg	29.10 Å
Envelope Rg envelope_rg	24.07 Å
Shape Rg shape_rg	23.92 Å
Total Rg total_rg	24.70 Å
Total atoms total_atoms	2366
Residues n_residues	297
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	84.8 Å
Rg (real space) rg_real	24.56 Å
Rg uncertainty (real space) rg_real_error	0.69 Å
I(0) (real space) i0_real	1.7960e+07
I(0) uncertainty (real space) i0_real_error	2.6370e+05
Rg (reciprocal space) rg_reciprocal	24.52 Å
I(0) (reciprocal space) i0_reciprocal	17960000.0000
Solution quality estimate total_estimate	0.8392
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.9 Å
Skewness Skewness skewness	0.470
Kurtosis Kurtosis kurtosis	-0.381
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4776000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.763; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.695; Smooth: 0.924

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

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

fit	/app/data/saxs_computation/gl/9glt/9glt.fit
pddf	/app/data/pr_computation/gl/9glt/9glt.pr.out
profile	/app/data/saxs_computation/gl/9glt/9glt.dat