SAXSdb — 1b72

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

PROTEIN (HOMEOBOX PROTEIN HOX-B1)

Homo sapiens

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 170–266	Fragment：HEXAPEPTIDE, HOMEODOMAIN Mutation：1 RESIDUE (MET) ADDED TO N-TERMINUS	;DNA (5'-D(APCPTPCPTPAPTPGPAPTPTPGPAPTPCPGPGPCPTPG)-3') ; × 1 ;DNA (5'-D(TPCPAPGPCPCPGPAPTPCPAPAPTPCPAPTPAPGPAPG)-3') ; × 1 PROTEIN (PBX1) × 1 （P40424）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；pH 8.0	Resolution 2.35 Å R-free 0.277

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	HXB1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–97； UniProt 170–266

PROTEIN (PBX1)

Homo sapiens

UniProt P40424

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 233–319	Fragment：HOMEODOMAIN	;DNA (5'-D(APCPTPCPTPAPTPGPAPTPTPGPAPTPCPGPGPCPTPG)-3') ; × 1 ;DNA (5'-D(TPCPAPGPCPCPGPAPTPCPAPAPTPCPAPTPAPGPAPG)-3') ; × 1 PROTEIN (HOMEOBOX PROTEIN HOX-B1) × 1 （P14653）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；pH 8.0	Resolution 2.35 Å R-free 0.277

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 1B72	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1PUF Crystal Structure of HoxA9 and Pbx1 homeodomains bound to DNA Deposited 2003-06-24	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 233–305（73 aa） Fragment：residues 233-305	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；292 K；PEG 4000, hepes, cobaltic hexamine, dithiothrietol, EDTA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K, pH 7.50	Resolution 1.90 Å R-free 0.268

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PBX1_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 1–87； UniProt 233–319

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	1b72
Deposition date deposition_date	1999-01-27
Structure title title	PBX1, HOMEOBOX PROTEIN HOX-B1/DNA TERNARY COMPLEX
Keywords keywords	HOMEODOMAIN, DNA, COMPLEX, DNA-BINDING PROTEIN, PROTEIN-DNA COMPLEX; PROTEIN/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	20.41 Å
Radius of gyration Rg (electron density) rg_electron	19.85 Å
Forward intensity I(0) i0	22461800.00
Molecular weight molecular_weight	28306.0 kDa
Excluded volume excluded_volume	32011 Å³
Envelope volume envelope_volume	41955 Å³
Hydration-shell volume shell_volume	18337 Å³
Envelope diameter envelope_diameter	71.5 Å
Shell Rg shell_rg	25.39 Å
Envelope Rg envelope_rg	19.97 Å
Shape Rg shape_rg	19.82 Å
Total Rg total_rg	20.56 Å
Total atoms total_atoms	1949
Residues n_residues	181
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	68.6 Å
Rg (real space) rg_real	20.42 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	2.2460e+07
I(0) uncertainty (real space) i0_real_error	3.0210e+05
Rg (reciprocal space) rg_reciprocal	20.42 Å
I(0) (reciprocal space) i0_reciprocal	22460000.0000
Solution quality estimate total_estimate	0.8046
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.5 Å
Skewness Skewness skewness	0.379
Kurtosis Kurtosis kurtosis	-0.271
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3062000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.000

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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(APCPTPCPTPAPTPGPAPTPTPGPAPTPCPGPGPCPTPG)-3') ;
Molecular weight formula_weight	6140.0 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	2010

ACTCTATGATTGATCGGCTG

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(TPCPAPGPCPCPGPAPTPCPAPAPTPCPAPTPAPGPAPG)-3') ;
Molecular weight formula_weight	6127.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

TCAGCCGATCAATCATAGAG

Entity 3 Entity 3 polymer

Description description	PROTEIN (HOMEOBOX PROTEIN HOX-B1)
Molecular weight formula_weight	11443.1 kDa
Mutation mutation	1 RESIDUE (MET) ADDED TO N-TERMINUS
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MEPNTPTARTFDWMKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKREREGG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	PROTEIN (PBX1)
Molecular weight formula_weight	10073.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAKTAVTATNVSAH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	61

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1b72a_
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.4.1.1 — Homeodomain

Domain ID domain_id	d1b72b_
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.4.1.1 — Homeodomain

CATH v4.4 (2 domains)

Domain ID domain_id	1b72A00
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	1b72B00
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 (1)

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Unit-cell length a length_a	58.670 Å
Unit-cell length b length_b	64.580 Å
Unit-cell length c length_c	81.910 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2430
R_work r_work	0.2430
R_free r_free	0.2770

fit	/app/data/saxs_computation/b7/1b72/1b72.fit
pddf	/app/data/pr_computation/b7/1b72/1b72.pr.out
profile	/app/data/saxs_computation/b7/1b72/1b72.dat

PBX1, HOMEOBOX PROTEIN HOX-B1/DNA TERNARY COMPLEX

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

PROTEIN (HOMEOBOX PROTEIN HOX-B1)

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (PBX1)

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)