SAXSdb — 2lo2

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

SAGA-associated factor 11

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 63–99	Fragment：SGF11-type zinc finger residues 63-99	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions：pH 7；285 K；Ionic strength (raw mmCIF value) 0.115；Pressure ambient NMR sample composition：0.7 mM [U-99% 13C; U-98% 15N] sgf11, 20 mM sodium phosphate, 75 mM sodium chloride, 1 mM DTT, 10 % D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 2LO2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3KIK Sgf11:Sus1 complex Deposited 2009-11-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 7–33（27 aa） Fragment：Sus1 binding region of Sgf11	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；3.2 M Na formate. See publication for details, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.10 Å R-free 0.231
3KIK Sgf11:Sus1 complex Deposited 2009-11-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 7–33（27 aa） Fragment：Sus1 binding region of Sgf11	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；3.2 M Na formate. See publication for details, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.10 Å R-free 0.231
3KIK Sgf11:Sus1 complex Deposited 2009-11-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 7–33（27 aa） Fragment：Sus1 binding region of Sgf11	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；3.2 M Na formate. See publication for details, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.10 Å R-free 0.231
3KIK Sgf11:Sus1 complex Deposited 2009-11-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 7–33（27 aa） Fragment：Sus1 binding region of Sgf11	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；3.2 M Na formate. See publication for details, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.10 Å R-free 0.231
3KJL Sgf11:Sus1 complex Deposited 2009-11-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2–33（32 aa） Fragment：Sus1-binding region	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；see publication, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.70 Å R-free 0.253
3KJL Sgf11:Sus1 complex Deposited 2009-11-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 2–33（32 aa） Fragment：Sus1-binding region	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；see publication, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.70 Å R-free 0.253
3KJL Sgf11:Sus1 complex Deposited 2009-11-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 2–33（32 aa） Fragment：Sus1-binding region	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；see publication, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.70 Å R-free 0.253
3KJL Sgf11:Sus1 complex Deposited 2009-11-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 2–33（32 aa） Fragment：Sus1-binding region	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；see publication, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.70 Å R-free 0.253
3M99 Structure of the Ubp8-Sgf11-Sgf73-Sus1 SAGA DUB module Deposited 2010-03-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–99（99 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；0.2M ammonium citrate, 18% PEG 3,350, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.300
3MHH Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module Deposited 2010-04-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–99（99 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；0.1 M Na Citrate (5.2), 16% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.45 Å R-free 0.273
3MHS Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde Deposited 2010-04-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–99（99 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M Hepes pH 6.5, 10% (w/v) PEG 8000, 20% (v/v) Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.89 Å R-free 0.208
4FIP Structure of the SAGA Ubp8(S144N)/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module Deposited 2012-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 1–72（72 aa） Fragment：UNP Residues 1-72 Chain G 1–72（72 aa） Fragment：UNP Residues 1-72	Not recorded	ZN ZINC ION × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；14% PEG3350, 0.18-0.22 M Tri-ammonium citrate, 8-14% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.69 Å R-free 0.264
4FJC Structure of the SAGA Ubp8/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module Deposited 2012-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 1–99（99 aa） Fragment：UNP Residues Sgf11 1-72 Chain G 1–99（99 aa） Fragment：UNP Residues Sgf11 1-72	Not recorded	ZN ZINC ION × 14 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；14% PEG3350, 0.18-0.22 M tri-ammonium citrate, 8-14% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.83 Å R-free 0.276
4FK5 Structure of the SAGA Ubp8(S144N)/Sgf11/Sus1/Sgf73 DUB module Deposited 2012-06-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–99（99 aa）	Not recorded	ZN ZINC ION × 8 GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；sodium citrate pH 5.2, 16% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.03 Å R-free 0.212
6AQR SAGA DUB module Ubp8(C146A)/Sgf11/Sus1/Sgf73 bound to monoubiquitin Deposited 2017-08-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–99（99 aa）	Not recorded	ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M HEPES pH 7.0 17% PEG3350 0.1 M ammonium sulfate	Resolution 2.10 Å R-free 0.249
6T9L SAGA DUB module bound to a ubiqitinated nucleosome Deposited 2019-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain M 1–99（99 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Solution were made from stock solution cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging	Resolution 3.60 Å

10 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SGF11_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–38； UniProt 63–99

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	2lo2
Deposition date deposition_date	2012-01-10
Structure title title	Solution structure of Sgf11(63-99) zinc finger domain
Keywords keywords	ZINC-FINGER, DEUBIQUITINATION, TRANSCRIPTION FACTOR, SAGA COMPLEX, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	11.82 Å
Radius of gyration Rg (electron density) rg_electron	11.92 Å
Forward intensity I(0) i0	158957000.00
Molecular weight molecular_weight	87384.0 kDa
Excluded volume excluded_volume	102490 Å³
Envelope volume envelope_volume	22131 Å³
Hydration-shell volume shell_volume	11856 Å³
Envelope diameter envelope_diameter	58.8 Å
Shell Rg shell_rg	21.74 Å
Envelope Rg envelope_rg	17.35 Å
Shape Rg shape_rg	11.95 Å
Total Rg total_rg	12.19 Å
Total atoms total_atoms	11820
Residues n_residues	760
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	31.9 Å
Rg (real space) rg_real	11.04 Å
Rg uncertainty (real space) rg_real_error	0.06 Å
I(0) (real space) i0_real	1.5190e+08
I(0) uncertainty (real space) i0_real_error	1.1450e+06
Rg (reciprocal space) rg_reciprocal	12.05 Å
I(0) (reciprocal space) i0_reciprocal	159000000.0000
Solution quality estimate total_estimate	0.6797
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	11.7 Å
Skewness Skewness skewness	0.396
Kurtosis Kurtosis kurtosis	-0.474
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	4.8360
Highest regularization parameter α highest_alpha	27150.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.003; Oscil: 0.993; Stabil: 0.979; Sysdev: 0.000; Positv: 1.000; Valcen: 0.921; Smooth: 0.000

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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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Description description	SAGA-associated factor 11
Molecular weight formula_weight	4308.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	11820

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/lo/2lo2/2lo2.fit
pddf	/app/data/pr_computation/lo/2lo2/2lo2.pr.out
profile	/app/data/saxs_computation/lo/2lo2/2lo2.dat

Solution structure of Sgf11(63-99) zinc finger domain

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

SAGA-associated factor 11

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)