1a5j

CHICKEN B-MYB DNA BINDING DOMAIN, REPEAT 2 AND REPEAT3, NMR, 32 STRUCTURES

Method: SOLUTION NMR D_max: 60.4 Å Quality: REASONABLE

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

B-MYB

Gallus gallus

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 79–186	Fragment：DNA BINDING DOMAIN, REPEAT 2 AND REPEAT 3	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6；288 K	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.

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

View Construct and Data Evidence

UniProt name	MYBB_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–110； UniProt 79–186

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1a5j
Deposition date deposition_date	1998-02-16
Structure title title	CHICKEN B-MYB DNA BINDING DOMAIN, REPEAT 2 AND REPEAT3, NMR, 32 STRUCTURES
Keywords keywords	DNA-BINDING PROTEIN, PROTOONCOGENE PRODUCT, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	23.91 Å
Radius of gyration Rg (electron density) rg_electron	24.30 Å
Forward intensity I(0) i0	2340620000.00
Molecular weight molecular_weight	413500.0 kDa
Excluded volume excluded_volume	520950 Å³
Envelope volume envelope_volume	155410 Å³
Hydration-shell volume shell_volume	41624 Å³
Envelope diameter envelope_diameter	108.8 Å
Shell Rg shell_rg	38.22 Å
Envelope Rg envelope_rg	30.86 Å
Shape Rg shape_rg	24.24 Å
Total Rg total_rg	24.87 Å
Total atoms total_atoms	59136
Residues n_residues	3520
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	60.4 Å
Rg (real space) rg_real	22.67 Å
Rg uncertainty (real space) rg_real_error	0.12 Å
I(0) (real space) i0_real	2.2330e+09
I(0) uncertainty (real space) i0_real_error	1.9260e+07
Rg (reciprocal space) rg_reciprocal	24.06 Å
I(0) (reciprocal space) i0_reciprocal	2341000000.0000
Solution quality estimate total_estimate	0.6410
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.0 Å
Skewness Skewness skewness	0.155
Kurtosis Kurtosis kurtosis	-1.033
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	2.6430
Highest regularization parameter α highest_alpha	829100.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.001; Oscil: 0.939; Stabil: 0.973; Sysdev: 0.000; Positv: 1.000; Valcen: 0.598; Smooth: 0.000

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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1a5ja1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.3 — Myb/SANT domain

Domain ID domain_id	d1a5ja2
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.3 — Myb/SANT domain

CATH v4.4 (2 domains)

Domain ID domain_id	1a5jA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	1a5jA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

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8. Citations (2)

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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	B-MYB
Molecular weight formula_weight	12958.9 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	59136

来源生物 organism	Gallus gallus
通用名 common_name	chicken
NCBI Class编号 ncbi_taxonomy_id	9031
宿主生物 host_organism	Escherichia coli

CHICKEN B-MYB DNA BINDING DOMAIN, REPEAT 2 AND REPEAT3, NMR, 32 STRUCTURES

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

B-MYB

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/a5/1a5j/1a5j.fit
pddf	/app/data/pr_computation/a5/1a5j/1a5j.pr.out
profile	/app/data/saxs_computation/a5/1a5j/1a5j.dat