SAXSdb — 1awc

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

PROTEIN (GA BINDING PROTEIN ALPHA)

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 Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 320–429	Fragment：ETS DOMAIN PLUS 30 C-TERMINAL RESIDUES	;DNA (5'-D(APAP(BRU)PGPAPCPCPGPGPAPAPGPTPAP(CBR)PAPCP(CBR)PGPGPA)-3') ; × 1 ;DNA (5'-D(TPTPCPCPGPGP(BRU)PGP(BRU)PAPCPTPTPCPCPGPGPTPCPAPT)-3') ; × 1 PROTEIN (GA BINDING PROTEIN BETA 1) × 1 （Q00420）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 9；100 MM BIS-TRIS PROPANE PH 9, 12 % PEG 1000, 5 MM COBALTIC HEXAMINE CHLORIDE, 1 MM DTT, 20 MM TRIS, 1 MM EDTA, 0.001 % SODIUM AZIDE, pH 9.0	Resolution 2.15 Å R-free 0.282

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 1AWC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1SXD Solution Structure of the Pointed (PNT) Domain from mGABPa Deposited 2004-03-30	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 168–254（87 aa） Fragment：PNT domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；303 K；Ionic strength (raw mmCIF value) 40 mM；Pressure ambient NMR measurement conditions pH 7.2；303 K；Ionic strength (raw mmCIF value) 40 mM；Pressure ambient NMR measurement conditions pH 7.2；303 K；Ionic strength (raw mmCIF value) 40 mM；Pressure ambient NMR sample composition 1mM GABPa U-15N,13C, 20mM phosphate buffer pH 7.2, 20mM NaCl, 2mM DTT, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM GABPa 100%15N,10%13C, 20mM phosphate buffer pH 7.2 20mM NaCl, 2mM DTT, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 2mM GABPa 100%15N, 20mM phosphate buffer pH 7.2 20mM NaCl, 2mM DTT, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2JUO GABPa OST domain Deposited 2007-08-31	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 35–121（87 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298.1 K NMR sample composition 20 mM sodium phosphate, 20 mM sodium chloride, 1 mM [U-100% 13C; U-100% 15N] GABPa OST, 2 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM [U-100% 15N] GABPa OST, 2 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM [U-10% 13C; U-100% 15N] GABPa OST, 2 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% 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	GABPA_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–110； UniProt 320–429

PROTEIN (GA BINDING PROTEIN BETA 1)

Mus musculus

UniProt Q00420

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 Heteromer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain B； UniProt 5–157	Fragment：ANKYRIN REPEAT DOMAIN	;DNA (5'-D(APAP(BRU)PGPAPCPCPGPGPAPAPGPTPAP(CBR)PAPCP(CBR)PGPGPA)-3') ; × 1 ;DNA (5'-D(TPTPCPCPGPGP(BRU)PGP(BRU)PAPCPTPTPCPCPGPGPTPCPAPT)-3') ; × 1 PROTEIN (GA BINDING PROTEIN ALPHA) × 1 （Q00422）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 9；100 MM BIS-TRIS PROPANE PH 9, 12 % PEG 1000, 5 MM COBALTIC HEXAMINE CHLORIDE, 1 MM DTT, 20 MM TRIS, 1 MM EDTA, 0.001 % SODIUM AZIDE, pH 9.0	Resolution 2.15 Å R-free 0.282

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	GABP2_MOUSE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 1–153； UniProt 5–157

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	1awc
Deposition date deposition_date	1997-10-01
Structure title title	MOUSE GABP ALPHA/BETA DOMAIN BOUND TO DNA
Keywords keywords	;COMPLEX (TRANSCRIPTION REGULATION-DNA), DNA-BINDING, NUCLEAR PROTEIN, ETS DOMAIN, ANKYRIN REPEATS, TRANSCRIPTION FACTOR, 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	25.04 Å
Radius of gyration Rg (electron density) rg_electron	23.73 Å
Forward intensity I(0) i0	44658400.00
Molecular weight molecular_weight	42584.0 kDa
Excluded volume excluded_volume	49214 Å³
Envelope volume envelope_volume	63132 Å³
Hydration-shell volume shell_volume	22886 Å³
Envelope diameter envelope_diameter	82.0 Å
Shell Rg shell_rg	29.91 Å
Envelope Rg envelope_rg	23.77 Å
Shape Rg shape_rg	23.66 Å
Total Rg total_rg	24.52 Å
Total atoms total_atoms	2920
Residues n_residues	300
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	78.9 Å
Rg (real space) rg_real	25.00 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	4.4660e+07
I(0) uncertainty (real space) i0_real_error	6.1960e+05
Rg (reciprocal space) rg_reciprocal	25.02 Å
I(0) (reciprocal space) i0_reciprocal	44660000.0000
Solution quality estimate total_estimate	0.9127
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.1 Å
Skewness Skewness skewness	0.213
Kurtosis Kurtosis kurtosis	-0.570
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3115000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.965; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.991

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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	;DNA (5'-D(APAP(BRU)PGPAPCPCPGPGPAPAPGPTPAP(CBR)PAPCP(CBR)PGPGP*A)-3') ;
Molecular weight formula_weight	6712.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D
Atom count atom_count	2966

AAUGACCGGAAGTACACCGGA

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(TPTPCPCPGPGP(BRU)PGP(BRU)PAPCPTPTPCPCPGPGPTPCPAP*T)-3') ;
Molecular weight formula_weight	6525.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

TTCCGGUGUACTTCCGGTCAT

Entity 3 Entity 3 polymer

Description description	PROTEIN (GA BINDING PROTEIN ALPHA)
Molecular weight formula_weight	13065.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

IQLWQFLLELLTDKDARDCISWVGDEGEFKLNQPELVAQKWGQRKNKPTMNYEKLSRALRYYYDGDMICKVQGKRFVYKFVCDLKTLIGYSAAELNRLVIECEQKKLARM

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	PROTEIN (GA BINDING PROTEIN BETA 1)
Molecular weight formula_weight	16834.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DLGKKLLEAARAGQDDEVRILMANGAPFTTDWLGTSPLHLAAQYGHFSTTEVLLRAGVSRDARTKVDRTPLHMAASEGHANIVEVLLKHGADVNAKDMLKMTALHWATEHNHQEVVELLIKYGADVHTQSKFCKTAFDISIDNGNEDLAEILQ

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	46

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1awca_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.21 — ets domain

Domain ID domain_id	d1awcb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.211 — beta-hairpin-alpha-hairpin repeat
Superfamily Superfamily superfamily	d.211.1 — Ankyrin repeat
Family Family family	d.211.1.1 — Ankyrin repeat

CATH v4.4 (2 domains)

Domain ID domain_id	1awcA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1awcB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

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8. Citations (1)

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Unit-cell length a length_a	201.600 Å
Unit-cell length b length_b	34.550 Å
Unit-cell length c length_c	59.260 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.83 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	—
R_work r_work	0.2110
R_free r_free	0.2820

fit	/app/data/saxs_computation/aw/1awc/1awc.fit
pddf	/app/data/pr_computation/aw/1awc/1awc.pr.out
profile	/app/data/saxs_computation/aw/1awc/1awc.dat

MOUSE GABP ALPHA/BETA DOMAIN BOUND TO DNA

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

PROTEIN (GA BINDING PROTEIN ALPHA)

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (GA BINDING PROTEIN BETA 1)

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)