SAXSdb — 2bwf

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

UBIQUITIN-LIKE PROTEIN DSK2

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 A； UniProt 1–75	Fragment：UBL DOMAIN, RESIDUES 1-75	FMT FORMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.00	Resolution 1.15 Å R-free 0.195
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–75	Fragment：UBL DOMAIN, RESIDUES 1-75	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.00	Resolution 1.15 Å R-free 0.195

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 2BWF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WR1 The complex structure of Dsk2p UBA with ubiquitin Deposited 2004-10-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 328–373（46 aa） Fragment：C-TERMINAL UBA DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 20mM potassium phosphate, 5mM potassium chloride NMR sample composition U-15N, 13C ubiquitin + DSK2-UBA complex (0.9mM) \| 20mM Phosphate buffer (pH 6.8); 5mM potassium chloride; 1mM EDTA; 5% D2O NMR sample composition U-15N, 13C DSK2-UBA + ubiquitin complex (1.0mM) \| 20mM Phosphate buffer (pH 6.8); 5mM potassium chloride; 1mM EDTA; 5% D2O	Resolution not provided
2BWB Crystal structure of the UBA domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 326–371（46 aa） Fragment：UBA DOMAIN, RESIDUES 326-371	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
2BWB Crystal structure of the UBA domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 326–371（46 aa） Fragment：UBA DOMAIN, RESIDUES 326-371	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
2BWB Crystal structure of the UBA domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 326–371（46 aa） Fragment：UBA DOMAIN, RESIDUES 326-371	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
2BWB Crystal structure of the UBA domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 326–371（46 aa） Fragment：UBA DOMAIN, RESIDUES 326-371	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
2BWB Crystal structure of the UBA domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 326–371（46 aa） Fragment：UBA DOMAIN, RESIDUES 326-371	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
2BWB Crystal structure of the UBA domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 326–371（46 aa） Fragment：UBA DOMAIN, RESIDUES 326-371	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
2BWB Crystal structure of the UBA domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 326–371（46 aa） Fragment：UBA DOMAIN, RESIDUES 326-371	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
2BWB Crystal structure of the UBA domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 326–371（46 aa） Fragment：UBA DOMAIN, RESIDUES 326-371	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
2BWB Crystal structure of the UBA domain of Dsk2 from S. cerevisiae Deposited 2005-07-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 326–371（46 aa） Fragment：UBA DOMAIN, RESIDUES 326-371	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1.6 M TRISODIUM CITRATE PH 7.0	Resolution 2.30 Å R-free 0.307
2BWE The crystal structure of the complex between the UBA and UBL domains of Dsk2 Deposited 2005-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain B 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain C 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain D 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain E 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain F 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain G 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain H 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain I 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain T 1–75（75 aa） Fragment：UBL DOMAIN, RESIDUES 1-75	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；277 K；10-15% METHOXY PEG 5K BUFFERED WITH 0.1M MES PH 6.5 AT 4C	Resolution 3.10 Å R-free 0.267
2BWE The crystal structure of the complex between the UBA and UBL domains of Dsk2 Deposited 2005-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain N 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain O 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain P 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain Q 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain R 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain U 1–75（75 aa） Fragment：UBL DOMAIN, RESIDUES 1-75	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；277 K；10-15% METHOXY PEG 5K BUFFERED WITH 0.1M MES PH 6.5 AT 4C	Resolution 3.10 Å R-free 0.267
2BWE The crystal structure of the complex between the UBA and UBL domains of Dsk2 Deposited 2005-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain J 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain K 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain L 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain M 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 324-327 Chain S 1–75（75 aa） Fragment：UBL DOMAIN, RESIDUES 1-75	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；277 K；10-15% METHOXY PEG 5K BUFFERED WITH 0.1M MES PH 6.5 AT 4C	Resolution 3.10 Å R-free 0.267
3M63 Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Dsk2 Deposited 2010-03-15	Different construct 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 1–75（75 aa） Fragment：UNP residues 1-75, Ubiquitin-like domain	Not recorded	1PE PENTAETHYLENE GLYCOL × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；298 K；16-18% PEG 3500 200 mM Tripotassium citrate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.270
4UN2 Crystal structure of the UBA domain of Dsk2 in complex with Ubiquitin Deposited 2014-05-23	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 328–373（46 aa） Fragment：UBA DOMAIN, RESIDUES 328-373	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.2M MAGNESIUM CHLORIDE, 0.1M TRIS PH 8.5, 20% PEG 8000	Resolution 1.51 Å R-free 0.196

5 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DSK2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–77； UniProt 1–75 Author chain B； PDBConstruct 3–77； UniProt 1–75

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	2bwf
Deposition date deposition_date	2005-07-13
Structure title title	Crystal structure of the UBL domain of Dsk2 from S. cerevisiae
Keywords keywords	SIGNALING PROTEIN, UBIQUITIN, UBA, SIGNALING PROTEINS; SIGNALING PROTEIN
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	17.92 Å
Radius of gyration Rg (electron density) rg_electron	17.04 Å
Forward intensity I(0) i0	5684730.00
Molecular weight molecular_weight	17244.0 kDa
Excluded volume excluded_volume	21580 Å³
Envelope volume envelope_volume	25286 Å³
Hydration-shell volume shell_volume	13071 Å³
Envelope diameter envelope_diameter	58.8 Å
Shell Rg shell_rg	21.99 Å
Envelope Rg envelope_rg	17.18 Å
Shape Rg shape_rg	17.01 Å
Total Rg total_rg	17.98 Å
Total atoms total_atoms	1216
Residues n_residues	153
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	59.5 Å
Rg (real space) rg_real	17.93 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	5.6850e+06
I(0) uncertainty (real space) i0_real_error	7.0890e+04
Rg (reciprocal space) rg_reciprocal	17.93 Å
I(0) (reciprocal space) i0_reciprocal	5685000.0000
Solution quality estimate total_estimate	0.8744
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.5 Å
Skewness Skewness skewness	0.332
Kurtosis Kurtosis kurtosis	-0.439
Angular range angular_range	— – 0.4450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1662000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.798; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.981

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	UBIQUITIN-LIKE PROTEIN DSK2
Molecular weight formula_weight	8634.7 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	1375

LDMSLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKSQP

来源 Source

来源生物 organism	SACCHAROMYCES CEREVISIAE
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 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	159

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2bwfa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.0 — automated matches

Domain ID domain_id	d2bwfb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2bwfA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	2bwfB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	49.415 Å
Unit-cell length b length_b	49.587 Å
Unit-cell length c length_c	58.771 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.150 Å
Low-resolution limit resolution_low	34.920 Å
R factor r_factor	0.1850
R_work r_work	0.1840
R_free r_free	0.1950

fit	/app/data/saxs_computation/bw/2bwf/2bwf.fit
pddf	/app/data/pr_computation/bw/2bwf/2bwf.pr.out
profile	/app/data/saxs_computation/bw/2bwf/2bwf.dat

Crystal structure of the UBL domain of Dsk2 from S. cerevisiae

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

UBIQUITIN-LIKE PROTEIN DSK2

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