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3onh

Crystal structure of UBA2ufd-Ubc9: insights into E1-E2 interactions in Sumo pathways

Method: X-RAY DIFFRACTION Dmax: 50.2 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin-activating enzyme E1-like

Saccharomyces cerevisiae

UniProt P52488

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 A； UniProt 439–563 Fragment：UNP residues 439-563 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；3M (NH4)2SO4, 1% MPD, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.60 Å R-free 0.178

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 3ONH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3ONG Crystal structure of UBA2ufd-Ubc9: insights into E1-E2 interactions in Sumo pathways Deposited 2010-08-28 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 439–563（125 aa） Fragment：UNP residues 439-563
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；20% PEG3350, 0.1 M Bis-Tris pH 5.5, 0.2 M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.251
3ONG Crystal structure of UBA2ufd-Ubc9: insights into E1-E2 interactions in Sumo pathways Deposited 2010-08-28 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 439–563（125 aa） Fragment：UNP residues 439-563
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；20% PEG3350, 0.1 M Bis-Tris pH 5.5, 0.2 M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.251

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UBA2_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–127； UniProt 439–563

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.

SAXS scattering curve SAXS Profile

SAXS profile for 3onh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3onh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3onh
Deposition date deposition_date2010-08-28
Structure title titleCrystal structure of UBA2ufd-Ubc9: insights into E1-E2 interactions in Sumo pathways
Keywords keywordsligase, SUMO conjugation, Ubc9; LIGASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.12 Å
Radius of gyration Rg (electron density) rg_electron13.56 Å
Forward intensity I(0) i03184310.00
Molecular weight molecular_weight12633.0 kDa
Excluded volume excluded_volume15876 ų
Envelope volume envelope_volume17419 ų
Hydration-shell volume shell_volume11169 ų
Envelope diameter envelope_diameter49.5 Å
Shell Rg shell_rg19.00 Å
Envelope Rg envelope_rg13.88 Å
Shape Rg shape_rg13.53 Å
Total Rg total_rg14.82 Å
Total atoms total_atoms885
Residues n_residues113
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax50.2 Å
Rg (real space) rg_real15.04 Å
Rg uncertainty (real space) rg_real_error0.28 Å
I(0) (real space) i0_real3.1840e+06
I(0) uncertainty (real space) i0_real_error3.5270e+04
Rg (reciprocal space) rg_reciprocal15.04 Å
I(0) (reciprocal space) i0_reciprocal3184000.0000
Solution quality estimate total_estimate0.7025
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.7 Å
Skewness Skewness skewness0.191
Kurtosis Kurtosis kurtosis-0.228
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha408100.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.798; Stabil: 1.000; Sysdev: 0.256; Positv: 1.000; Valcen: 1.000; Smooth: 0.965
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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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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id3onhA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
Homologous superfamily homologous superfamily20 — Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3
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8. Citations (1)

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9. Files and Curves (10)