SAXSdb — 4e68

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

Signal transducer and activator of transcription 3

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 127–722	Fragment：STAT3 Core Fragment, residues (127-722)	;DNA (5'-D(TPGPCPAPTPTPTPCPCPCPGPTPAPAPAPTPCPT)-3') ; × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；0.005M MgSO4, 0.1M ammonium acetate, 10% glycerol, 0.05M MES pH 5.6, 0.25M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.58 Å R-free 0.273

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 4E68	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BG1 TRANSCRIPTION FACTOR STAT3B/DNA COMPLEX Deposited 1998-06-03	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 127–722（596 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.25 Å R-free 0.301
3CWG Unphosphorylated mouse STAT3 core fragment Deposited 2008-04-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 127–688（562 aa） Fragment：STAT3 Core Fragment, UNP residues (127-688)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；277 K；0.1M Bis-tris, 0.5M ammonium sulfate, 12% PEG3350, 0.1mM KCl, 0.05M NaI, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.05 Å R-free 0.269
3CWG Unphosphorylated mouse STAT3 core fragment Deposited 2008-04-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 127–688（562 aa） Fragment：STAT3 Core Fragment, UNP residues (127-688)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；277 K；0.1M Bis-tris, 0.5M ammonium sulfate, 12% PEG3350, 0.1mM KCl, 0.05M NaI, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.05 Å R-free 0.269
4ZIA Crystal Structure of STAT3 N-terminal domain Deposited 2015-04-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3–127（125 aa） Fragment：N-terminal domain (UNP residues 3-127) Chain B 3–127（125 aa） Fragment：N-terminal domain (UNP residues 3-127)	Not recorded	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；20% v/v PEG 3350, 0.2M magnesium formate	Resolution 2.70 Å R-free 0.270
4ZIA Crystal Structure of STAT3 N-terminal domain Deposited 2015-04-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 3–127（125 aa） Fragment：N-terminal domain (UNP residues 3-127) Chain D 3–127（125 aa） Fragment：N-terminal domain (UNP residues 3-127)	Not recorded	FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；20% v/v PEG 3350, 0.2M magnesium formate	Resolution 2.70 Å R-free 0.270
4ZIA Crystal Structure of STAT3 N-terminal domain Deposited 2015-04-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 3–127（125 aa） Fragment：N-terminal domain (UNP residues 3-127)	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；20% v/v PEG 3350, 0.2M magnesium formate	Resolution 2.70 Å R-free 0.270

3 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	STAT3_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–596； UniProt 127–722

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	4e68
Deposition date deposition_date	2012-03-15
Structure title title	Unphosphorylated STAT3B core protein binding to dsDNA
Keywords keywords	;SH2 Domain, Protein DNA Complex, Signal Transducer, Activator of Transcription, Duplex DNA, Nucleus, Cytosol, TRANSCRIPTION-DNA complex ;; TRANSCRIPTION/DNA
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	34.39 Å
Radius of gyration Rg (electron density) rg_electron	34.74 Å
Forward intensity I(0) i0	81454100.00
Molecular weight molecular_weight	69531.0 kDa
Excluded volume excluded_volume	86172 Å³
Envelope volume envelope_volume	118240 Å³
Hydration-shell volume shell_volume	31549 Å³
Envelope diameter envelope_diameter	144.7 Å
Shell Rg shell_rg	36.62 Å
Envelope Rg envelope_rg	35.66 Å
Shape Rg shape_rg	34.71 Å
Total Rg total_rg	34.96 Å
Total atoms total_atoms	4859
Residues n_residues	577
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	136.2 Å
Rg (real space) rg_real	34.89 Å
Rg uncertainty (real space) rg_real_error	1.77 Å
I(0) (real space) i0_real	8.1450e+07
I(0) uncertainty (real space) i0_real_error	1.6080e+06
Rg (reciprocal space) rg_reciprocal	34.58 Å
I(0) (reciprocal space) i0_reciprocal	81430000.0000
Solution quality estimate total_estimate	0.7518
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.6 Å
Skewness Skewness skewness	0.765
Kurtosis Kurtosis kurtosis	0.344
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15210000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.434; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.497; Smooth: 0.969

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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	;DNA (5'-D(TPGPCPAPTPTPTPCPCPCPGPTPAPAPAPTPCPT)-3') ;
Molecular weight formula_weight	5441.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B
Atom count atom_count	4998

TGCATTTCCCGTAAATCT

Entity 2 Entity 2 polymer

Description description	Signal transducer and activator of transcription 3
Molecular weight formula_weight	68135.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

GQANHPTAAVVTEKQQMLEQHLQDVRKRVQDLEQKMKVVENLQDDFDFNYKTLKSQGDMQDLNGNNQSVTRQKMQQLEQMLTALDQMRRSIVSELAGLLSAMEYVQKTLTDEELADWKRRQQIACIGGPPNICLDRLENWITSLAESQLQTRQQIKKLEELQQKVSYKGDPIVQHRPMLEERIVELFRNLMKSAFVVERQPCMPMHPDRPLVIKTGVQFTTKVRLLVKFPELNYQLKIKVCIDKDSGDVAALRGSRKFNILGTNTKVMNMEESNNGSLSAEFKHLTLREQRCGNGGRANCDASLIVTEELHLITFETEVYHQGLKIDLETHSLPVVVISNICQMPNAWASILWYNMLTNNPKNVNFFTKPPIGTWDQVAEVLSWQFSSTTKRGLSIEQLTTLAEKLLGPGVNYSGCQITWAKFCKENMAGKGFSFWVWLDNIIDLVKKYILALWNEGYIMGFISKERERAILSTKPPGTFLLRFSESSKEGGVTFTWVEKDISGSTQIQSVEPYTKQQLNNMSFAEIIMGYKIMDATNILVSPLVYLYPDIPKEEAFGKYCRPESQEHPEADPGSAAPYLKTKFICVTPFIDAVWK

来源 Source

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	139

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4e68A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	20 — STAT transcription factor, all-alpha domain

Domain ID domain_id	4e68A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	630 — STAT transcription factor, DNA-binding domain

Domain ID domain_id	4e68A03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	4e68A04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

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8. Citations (1)

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Unit-cell length a length_a	174.140 Å
Unit-cell length b length_b	174.140 Å
Unit-cell length c length_c	79.290 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	I 41
Space-group number int_tables_number	80
Crystal system crystal_system	—

Resolution resolution	2.585 Å
Low-resolution limit resolution_low	14.980 Å
R factor r_factor	0.2278
R_work r_work	0.2253
R_free r_free	0.2733

fit	/app/data/saxs_computation/e6/4e68/4e68.fit
pddf	/app/data/pr_computation/e6/4e68/4e68.pr.out
profile	/app/data/saxs_computation/e6/4e68/4e68.dat

Unphosphorylated STAT3B core protein binding to dsDNA

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

Signal transducer and activator of transcription 3

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)