SAXSdb — 1ilf

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

CORE-BINDING FACTOR

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–141	Fragment：BETA-SUBUNIT	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.6；297 K；Ionic strength (raw mmCIF value) 150mM sodium chloride；Pressure 1 NMR sample composition：1.6mM CBFb U-15N, 13C \| 25mM phosphate buffer, 3mM DTT, 100 % D2O NMR sample composition：1.6mM CBFb U-15N \| 25mM phosphate buffer, 3mM DTT, 10 % D2O NMR sample composition：0.8mM CBFb \| 25mM phosphate buffer,3mM DTT, 100 % 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 1ILF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1IO4 CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN-CBFBETA CORE DOMAIN HETERODIMER AND C/EBPBETA BZIP HOMODIMER BOUND TO A DNA FRAGMENT FROM THE CSF-1R PROMOTER Deposited 2001-01-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain D 1–141（141 aa） Fragment：CORE DOMAIN	Not recorded	AU GOLD ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；297 K；0.2 M potassium chloride, 0.01 M magnesium chloride, 0.01 M DTT, 4.5% V/V PEG 8000, 1% V/V glycerol, 1% V/V MPD, 0.05 M MES buffer pH 5.6, pH 5.60, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 3.00 Å R-free 0.299
2JHB CORE BINDING FACTOR BETA Deposited 1999-03-17	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–141（141 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；293 K；Pressure 1	Resolution not provided
3WTS Crystal structure of the complex comprised of ETS1, RUNX1, CBFBETA, and the tcralpha gene enhancer DNA Deposited 2014-04-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain B 1–142（142 aa） Fragment：UNP RESIDUES 1-142	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；10% PEG 4000, 0.1M AMMONIUM ACETATE, 0.05M TRIS HCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.35 Å R-free 0.279
3WTS Crystal structure of the complex comprised of ETS1, RUNX1, CBFBETA, and the tcralpha gene enhancer DNA Deposited 2014-04-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain G 1–142（142 aa） Fragment：UNP RESIDUES 1-142	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；10% PEG 4000, 0.1M AMMONIUM ACETATE, 0.05M TRIS HCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.35 Å R-free 0.279
3WTT Crystal structure of the complex comprised of phosphorylated ETS1, RUNX1, CBFBETA, and the tcralpha gene enhancer DNA Deposited 2014-04-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain B 1–142（142 aa） Fragment：UNP RESIDUES 1-142	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；10% PEG 4000, 0.25M AMMONIUM ACETATE, 0.05M SODIUM ACETATE, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.35 Å R-free 0.277
3WTT Crystal structure of the complex comprised of phosphorylated ETS1, RUNX1, CBFBETA, and the tcralpha gene enhancer DNA Deposited 2014-04-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain G 1–142（142 aa） Fragment：UNP RESIDUES 1-142	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；10% PEG 4000, 0.25M AMMONIUM ACETATE, 0.05M SODIUM ACETATE, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.35 Å R-free 0.277
3WTU Crystal structure of the complex comprised of ETS1 (V170A), RUNX1, CBFBETA, and the tcralpha gene enhancer DNA Deposited 2014-04-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain B 1–142（142 aa） Fragment：UNP RESIDUES 1-142	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；4% PEG 8000, 0.1M AMMONIUM ACETATE, 0.02M MAGNESIUM CHLORIDE, 0.05M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.70 Å R-free 0.282
3WTU Crystal structure of the complex comprised of ETS1 (V170A), RUNX1, CBFBETA, and the tcralpha gene enhancer DNA Deposited 2014-04-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain G 1–142（142 aa） Fragment：UNP RESIDUES 1-142	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；4% PEG 8000, 0.1M AMMONIUM ACETATE, 0.02M MAGNESIUM CHLORIDE, 0.05M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.70 Å R-free 0.282
3WTV Crystal structure of the complex comprised of ETS1(V170G), RUNX1, CBFBETA, and the tcralpha gene enhancer DNA Deposited 2014-04-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain B 1–142（142 aa） Fragment：UNP RESIDUES 1-142	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；4% PEG 8000, 0.1M AMMONIUM ACETATE, 0.02M MAGNESIUM CHLORIDE, 0.05M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.70 Å R-free 0.284
3WTV Crystal structure of the complex comprised of ETS1(V170G), RUNX1, CBFBETA, and the tcralpha gene enhancer DNA Deposited 2014-04-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain G 1–142（142 aa） Fragment：UNP RESIDUES 1-142	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；4% PEG 8000, 0.1M AMMONIUM ACETATE, 0.02M MAGNESIUM CHLORIDE, 0.05M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.70 Å R-free 0.284
3WTW Crystal structure of the complex comprised of ETS1(K167A), RUNX1, CBFBETA, and the tcralpha gene enhancer DNA Deposited 2014-04-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain B 1–142（142 aa） Fragment：UNP RESIDUES 1-142	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；12% ISOPROPANOL, 0.02M MAGNESIUM CHLORIDE, 0.05M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.90 Å R-free 0.264
3WTW Crystal structure of the complex comprised of ETS1(K167A), RUNX1, CBFBETA, and the tcralpha gene enhancer DNA Deposited 2014-04-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain G 1–142（142 aa） Fragment：UNP RESIDUES 1-142	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；12% ISOPROPANOL, 0.02M MAGNESIUM CHLORIDE, 0.05M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.90 Å R-free 0.264
3WTX Crystal structure of the complex comprised of ETS1(Y329A), RUNX1, CBFBETA, and the tcralpha gene enhancer DNA Deposited 2014-04-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain B 1–142（142 aa） Fragment：UNP RESIDUES 1-142	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；298 K；10% PEG 4000, 0.25M AMMONIUM ACETATE, 0.05M SODIUM ACETATE PH5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.80 Å R-free 0.271
3WTX Crystal structure of the complex comprised of ETS1(Y329A), RUNX1, CBFBETA, and the tcralpha gene enhancer DNA Deposited 2014-04-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain G 1–142（142 aa） Fragment：UNP RESIDUES 1-142	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；298 K；10% PEG 4000, 0.25M AMMONIUM ACETATE, 0.05M SODIUM ACETATE PH5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.80 Å R-free 0.271
3WTY Crystal structure of the complex comprised of ETS1(G333P), RUNX1, CBFBETA, and the tcralpha gene enhancer DNA Deposited 2014-04-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain B 1–142（142 aa） Fragment：UNP RESIDUES 1-142	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；298 K；4% PEG 4000, 0.25M AMMONIUM ACETATE, 0.05M SODIUM ACETATE, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.70 Å R-free 0.268
3WTY Crystal structure of the complex comprised of ETS1(G333P), RUNX1, CBFBETA, and the tcralpha gene enhancer DNA Deposited 2014-04-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain G 1–142（142 aa） Fragment：UNP RESIDUES 1-142	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；298 K；4% PEG 4000, 0.25M AMMONIUM ACETATE, 0.05M SODIUM ACETATE, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.70 Å R-free 0.268

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

View Construct and Data Evidence

UniProt name	PEBB_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–141； UniProt 1–141

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	1ilf
Deposition date deposition_date	2001-05-08
Structure title title	NMR STRUCTURE OF APO CBFB
Keywords keywords	partially open beta barrel, 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	16.77 Å
Radius of gyration Rg (electron density) rg_electron	16.19 Å
Forward intensity I(0) i0	2615470000.00
Molecular weight molecular_weight	414690.0 kDa
Excluded volume excluded_volume	510130 Å³
Envelope volume envelope_volume	37491 Å³
Hydration-shell volume shell_volume	17496 Å³
Envelope diameter envelope_diameter	61.4 Å
Shell Rg shell_rg	24.17 Å
Envelope Rg envelope_rg	18.42 Å
Shape Rg shape_rg	16.17 Å
Total Rg total_rg	16.37 Å
Total atoms total_atoms	57250
Residues n_residues	3525
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	55.7 Å
Rg (real space) rg_real	16.75 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	2.6150e+09
I(0) uncertainty (real space) i0_real_error	3.0170e+07
Rg (reciprocal space) rg_reciprocal	16.75 Å
I(0) (reciprocal space) i0_reciprocal	2615000000.0000
Solution quality estimate total_estimate	0.7542
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.1 Å
Skewness Skewness skewness	0.248
Kurtosis Kurtosis kurtosis	-0.461
Angular range angular_range	— – 0.4750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	659400.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 0.394; Positv: 1.000; Valcen: 0.981; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ilfa_
Class class	b — All beta proteins
Fold Fold fold	b.54 — Core binding factor beta, CBF
Superfamily Superfamily superfamily	b.54.1 — Core binding factor beta, CBF
Family Family family	b.54.1.1 — Core binding factor beta, CBF

CATH v4.4 (1 domains)

Domain ID domain_id	1ilfA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	250 — Polyomavirus Enhancer Binding Protein 2; Chain: A;
Homologous superfamily homologous superfamily	10 — Core binding factor, beta subunit

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	CORE-BINDING FACTOR
Molecular weight formula_weight	16613.6 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	57250

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)

NMR STRUCTURE OF APO CBFB

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

CORE-BINDING FACTOR

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/il/1ilf/1ilf.fit
pddf	/app/data/pr_computation/il/1ilf/1ilf.pr.out
profile	/app/data/saxs_computation/il/1ilf/1ilf.dat