SAXSdb — 4zia

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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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 3–127 Chain B； UniProt 3–127	Fragment：N-terminal domain (UNP residues 3-127)	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 3–127 Chain D； UniProt 3–127	Fragment：N-terminal domain (UNP residues 3-127)	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
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 3–127	Fragment：N-terminal domain (UNP residues 3-127)	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

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 4ZIA	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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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
4E68 Unphosphorylated STAT3B core protein binding to dsDNA Deposited 2012-03-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 127–722（596 aa） Fragment：STAT3 Core Fragment, residues (127-722)	Not recorded	No recorded non-water small molecule	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

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	STAT3_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–129； UniProt 3–127 Author chain B； PDBConstruct 5–129； UniProt 3–127 Author chain C； PDBConstruct 5–129； UniProt 3–127 Author chain D； PDBConstruct 5–129； UniProt 3–127 Author chain E； PDBConstruct 5–129； UniProt 3–127

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	4zia
Deposition date deposition_date	2015-04-28
Structure title title	Crystal Structure of STAT3 N-terminal domain
Keywords keywords	STAT N-terminal domain, TRANSCRIPTION; TRANSCRIPTION
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	31.79 Å
Radius of gyration Rg (electron density) rg_electron	31.33 Å
Forward intensity I(0) i0	83701500.00
Molecular weight molecular_weight	71927.0 kDa
Excluded volume excluded_volume	89747 Å³
Envelope volume envelope_volume	115160 Å³
Hydration-shell volume shell_volume	32181 Å³
Envelope diameter envelope_diameter	117.0 Å
Shell Rg shell_rg	36.40 Å
Envelope Rg envelope_rg	31.22 Å
Shape Rg shape_rg	31.31 Å
Total Rg total_rg	31.82 Å
Total atoms total_atoms	5086
Residues n_residues	601
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	109.4 Å
Rg (real space) rg_real	31.83 Å
Rg uncertainty (real space) rg_real_error	0.96 Å
I(0) (real space) i0_real	8.3700e+07
I(0) uncertainty (real space) i0_real_error	1.3320e+06
Rg (reciprocal space) rg_reciprocal	31.82 Å
I(0) (reciprocal space) i0_reciprocal	83700000.0000
Solution quality estimate total_estimate	0.8853
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.2 Å
Skewness Skewness skewness	0.317
Kurtosis Kurtosis kurtosis	-0.432
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13240000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.954

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Signal transducer and activator of transcription 3
Molecular weight formula_weight	15215.0 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	5149

GPGSQWNQLQQLDTRYLEQLHQLYSDSFPMELRQFLAPWIESQDWAYAASKESHATLVFHNLLGEIDQQYSRFLQESNVLYQHNLRRIKQFLQSRYLEKPMEIARIVARCLWEESRLLQTAATAAQQGG

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 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	63

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7. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d4ziaa1
Class class	a — All alpha proteins
Fold Fold fold	a.90 — Transcription factor STAT-4 N-domain
Superfamily Superfamily superfamily	a.90.1 — Transcription factor STAT-4 N-domain
Family Family family	a.90.1.0 — automated matches

Domain ID domain_id	d4ziaa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4ziab1
Class class	a — All alpha proteins
Fold Fold fold	a.90 — Transcription factor STAT-4 N-domain
Superfamily Superfamily superfamily	a.90.1 — Transcription factor STAT-4 N-domain
Family Family family	a.90.1.0 — automated matches

Domain ID domain_id	d4ziab2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4ziac1
Class class	a — All alpha proteins
Fold Fold fold	a.90 — Transcription factor STAT-4 N-domain
Superfamily Superfamily superfamily	a.90.1 — Transcription factor STAT-4 N-domain
Family Family family	a.90.1.0 — automated matches

Domain ID domain_id	d4ziac2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4ziad1
Class class	a — All alpha proteins
Fold Fold fold	a.90 — Transcription factor STAT-4 N-domain
Superfamily Superfamily superfamily	a.90.1 — Transcription factor STAT-4 N-domain
Family Family family	a.90.1.0 — automated matches

Domain ID domain_id	d4ziad2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4ziae1
Class class	a — All alpha proteins
Fold Fold fold	a.90 — Transcription factor STAT-4 N-domain
Superfamily Superfamily superfamily	a.90.1 — Transcription factor STAT-4 N-domain
Family Family family	a.90.1.0 — automated matches

Domain ID domain_id	d4ziae2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (5 domains)

Domain ID domain_id	4ziaA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	532 — Transcription Factor, Stat-4
Homologous superfamily homologous superfamily	10 — STAT transcription factor, N-terminal domain

Domain ID domain_id	4ziaB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	532 — Transcription Factor, Stat-4
Homologous superfamily homologous superfamily	10 — STAT transcription factor, N-terminal domain

Domain ID domain_id	4ziaC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	532 — Transcription Factor, Stat-4
Homologous superfamily homologous superfamily	10 — STAT transcription factor, N-terminal domain

Domain ID domain_id	4ziaD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	532 — Transcription Factor, Stat-4
Homologous superfamily homologous superfamily	10 — STAT transcription factor, N-terminal domain

Domain ID domain_id	4ziaE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	532 — Transcription Factor, Stat-4
Homologous superfamily homologous superfamily	10 — STAT transcription factor, N-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	109.012 Å
Unit-cell length b length_b	109.012 Å
Unit-cell length c length_c	154.300 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	40

Space group space_group	P 41 2 2
Space-group number int_tables_number	91
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2362
R_free r_free	0.2701

fit	/app/data/saxs_computation/zi/4zia/4zia.fit
pddf	/app/data/pr_computation/zi/4zia/4zia.pr.out
profile	/app/data/saxs_computation/zi/4zia/4zia.dat

Crystal Structure of STAT3 N-terminal domain

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