SAXSdb — 7yb4

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

Homeobox protein extradenticle

Drosophila melanogaster

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 238–300	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 5.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition：0.6 mM [U-13C; U-15N] Homeobox protein Extradenticle, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.6 mM [U-13C; U-15N] Homeobox protein Extradenticle, 90% H2O/10% D2O \| 90% H2O/10% 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 7YB4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B8I STRUCTURE OF THE HOMEOTIC UBX/EXD/DNA TERNARY COMPLEX Deposited 1999-02-01	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 238–300（63 aa） Fragment：HOMEODOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；0.6M AMMONIUM PHOSPHATE, pH 4.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.40 Å R-free 0.304
2R5Y Structure of Scr/Exd complex bound to a consensus Hox-Exd site Deposited 2007-09-04	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 238–300（63 aa） Fragment：Homeobox TALE-type DNA-binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.7；277 K；20% MPD, 10-14% PEG 4000, 0.2M sodium acetate, 0.2M potassium chloride, 0.1M Tris , pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.299
2R5Z Structure of Scr/Exd complex bound to a DNA sequence derived from the fkh gene Deposited 2007-09-04	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 238–300（63 aa） Fragment：Homeobox TALE-type DNA-binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.7；10-14 % PEG 4K, 20 % MPD, 0.1 M Tris, pH 8.7-8.9, 0.2 M Sodium Acetate, 0.2 M Potassium Chloride	Resolution 2.60 Å R-free 0.303
4CYC CRYSTAL STRUCTURE OF A UBX-EXD-DNA COMPLEX INCLUDING THE HEXAPEPTIDE AND UBDA MOTIFS Deposited 2014-04-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 238–312（75 aa） Fragment：HOMEODOMAIN RESIDUES 238-312	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 M AMMONIUM PHOSPHATE, pH 7.5	Resolution 2.36 Å R-free 0.227
4UUS CRYSTAL STRUCTURE OF A UBX-EXD-DNA COMPLEX INCLUDING THE UBDA MOTIF Deposited 2014-07-31	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 238–312（75 aa） Fragment：HOMEODOMAIN RESIDUES 238-312	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；0.2M AMONIUM SULFATE, 0.1 M TRI-SODIUM-CITRATE PH 4.5, 4% P4000	Resolution 2.55 Å R-free 0.239
4UUS CRYSTAL STRUCTURE OF A UBX-EXD-DNA COMPLEX INCLUDING THE UBDA MOTIF Deposited 2014-07-31	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain F 238–312（75 aa） Fragment：HOMEODOMAIN RESIDUES 238-312	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；0.2M AMONIUM SULFATE, 0.1 M TRI-SODIUM-CITRATE PH 4.5, 4% P4000	Resolution 2.55 Å R-free 0.239
5ZJQ Structure of AbdB/Exd complex bound to a 'Red14' DNA sequence Deposited 2018-03-22	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 237–310（74 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；200mM MgCl2, 0.1M Tris pH 5.8, 17.5% PEG 4000, 5% glycerol	Resolution 2.44 Å R-free 0.252
5ZJR Structure of AbdB/Exd complex bound to a 'Magenta14' DNA sequence Deposited 2018-03-22	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 237–310（74 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；90mM MgCl2, 0.1M Tris pH9.0, 22% PEG 3350	Resolution 3.03 Å R-free 0.288
5ZJS Structure of AbdB/Exd complex bound to a 'Blue14' DNA sequence Deposited 2018-03-22	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 237–310（74 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；200mM MgCl2, 0.1M Tris pH 5.8, 17.5% PEG 3350, 2.5% glycerol	Resolution 2.90 Å R-free 0.281
5ZJT Structure of AbdB/Exd complex bound to a 'Black14' DNA sequence Deposited 2018-03-22	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 237–310（74 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M Sodium citrate pH 5.3, 25% PEG 3350	Resolution 2.40 Å R-free 0.276

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EXD_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–67； UniProt 238–300

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	7yb4
Deposition date deposition_date	2022-06-28
Structure title title	Solution structure of homeodomain of EXTRADENTICLE
Keywords keywords	Transcription factor, Homeotic protein, DNA binding domain, 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	13.47 Å
Radius of gyration Rg (electron density) rg_electron	13.37 Å
Forward intensity I(0) i0	385424000.00
Molecular weight molecular_weight	159180.0 kDa
Excluded volume excluded_volume	197160 Å³
Envelope volume envelope_volume	34384 Å³
Hydration-shell volume shell_volume	15554 Å³
Envelope diameter envelope_diameter	64.1 Å
Shell Rg shell_rg	24.90 Å
Envelope Rg envelope_rg	20.15 Å
Shape Rg shape_rg	13.29 Å
Total Rg total_rg	13.96 Å
Total atoms total_atoms	22400
Residues n_residues	1340
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	37.0 Å
Rg (real space) rg_real	12.68 Å
Rg uncertainty (real space) rg_real_error	0.07 Å
I(0) (real space) i0_real	3.6920e+08
I(0) uncertainty (real space) i0_real_error	3.1740e+06
Rg (reciprocal space) rg_reciprocal	13.63 Å
I(0) (reciprocal space) i0_reciprocal	385400000.0000
Solution quality estimate total_estimate	0.6618
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	14.1 Å
Skewness Skewness skewness	0.388
Kurtosis Kurtosis kurtosis	-0.246
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	3.4170
Highest regularization parameter α highest_alpha	170500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.002; Oscil: 0.903; Stabil: 0.967; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; 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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8. Citations (1)

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Description description	Homeobox protein extradenticle
Molecular weight formula_weight	7967.0 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	22400

来源生物 organism	Drosophila melanogaster
通用名 common_name	fruit fly
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Escherichia coli BL21(DE3)

fit	/app/data/saxs_computation/yb/7yb4/7yb4.fit
pddf	/app/data/pr_computation/yb/7yb4/7yb4.pr.out
profile	/app/data/saxs_computation/yb/7yb4/7yb4.dat

Solution structure of homeodomain of EXTRADENTICLE

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

Homeobox protein extradenticle

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)