SAXSdb — 4zqa

▼

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

Sin3 histone deacetylase corepressor complex component SDS3

Mus musculus

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 90–172	Fragment：UNP residues 90-172	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.4；287 K；15% ethanol (v/v), 200 mM MgCl2, and 100 mM imidazole	Resolution 1.65 Å R-free 0.209

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 4ZQA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2N2H Solution structure of Sds3 in complex with Sin3A Deposited 2015-05-08	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 A 205–228（24 aa） Fragment：UNP residues 205-228	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；303 K；Ionic strength (raw mmCIF value) 0.12；Pressure ambient NMR sample composition 0.5-1 mM [U-100% 13C; U-100% 15N] Sin3HID, 0.5-1 mM Sds3SID, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5-1 mM [U-100% 13C; U-100% 15N] Sds3SID, 0.5-1 mM Sin3HID, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
7SXI Solution Structure of Sds3 Capped Tudor Domain Deposited 2021-11-23	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 250–326（77 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.07；Pressure 1 NMR sample composition 0.35 mM [U-100% 15N] Sds3 CTD, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.35 mM [U-100% 13C; U-100% 15N] Sds3 CTD, 100% D2O \| 100% D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	SDS3_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–86； UniProt 90–172

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4zqa
Deposition date deposition_date	2015-05-08
Structure title title	Crystal Structure of the Sds3 Dimerization Domain
Keywords keywords	transcription repression, histone deacetylase complex, coiled-coil, corepressor complex, TRANSCRIPTION REPRESSOR; TRANSCRIPTION REPRESSOR
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	34.75 Å
Radius of gyration Rg (electron density) rg_electron	36.33 Å
Forward intensity I(0) i0	1942390.00
Molecular weight molecular_weight	10361.0 kDa
Excluded volume excluded_volume	13020 Å³
Envelope volume envelope_volume	21778 Å³
Hydration-shell volume shell_volume	7021 Å³
Envelope diameter envelope_diameter	128.4 Å
Shell Rg shell_rg	29.46 Å
Envelope Rg envelope_rg	36.97 Å
Shape Rg shape_rg	36.22 Å
Total Rg total_rg	35.79 Å
Total atoms total_atoms	726
Residues n_residues	86
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

▼

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

Maximum dimension Dmax dmax	125.5 Å
Rg (real space) rg_real	35.82 Å
Rg uncertainty (real space) rg_real_error	2.00 Å
I(0) (real space) i0_real	1.9420e+06
I(0) uncertainty (real space) i0_real_error	3.5710e+04
Rg (reciprocal space) rg_reciprocal	35.15 Å
I(0) (reciprocal space) i0_reciprocal	1941000.0000
Solution quality estimate total_estimate	0.5584
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	10.9 Å
Skewness Skewness skewness	0.614
Kurtosis Kurtosis kurtosis	-0.512
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	96230.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.002; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.012; Smooth: 0.243

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▶

8. Citations (1)

▶

Unit-cell length a length_a	44.460 Å
Unit-cell length b length_b	49.390 Å
Unit-cell length c length_c	106.510 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	33.000 Å
R factor r_factor	0.1626
R_work r_work	0.1600
R_free r_free	0.2090

Description description	Sin3 histone deacetylase corepressor complex component SDS3
Molecular weight formula_weight	10396.9 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	866

Crystal Structure of the Sds3 Dimerization Domain

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

Sin3 histone deacetylase corepressor complex component SDS3

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	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
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	120

fit	/app/data/saxs_computation/zq/4zqa/4zqa.fit
pddf	/app/data/pr_computation/zq/4zqa/4zqa.pr.out
profile	/app/data/saxs_computation/zq/4zqa/4zqa.dat