SAXSdb — 6tyy

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

Protein hedgehog

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 258–403	Mutation：D46H Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M Hepes, pH 7.5, 3.4 M sodium formate	Resolution 1.36 Å R-free 0.195

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 6TYY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AT0 17-kDA fragment of hedgehog C-terminal autoprocessing domain Deposited 1997-08-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 258–402（145 aa） Fragment：17-KDA FRAGMENT OF C-TERMINAL DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；20% PEG 3350, 80 mM AMMONIUM SULFATE, 10 mM SODIUM CACODYLATE pH 5.8	Resolution 1.90 Å R-free 0.275
2IBG Crystal Structure of Hedgehog Bound to the FNIII Domains of Ihog Deposited 2006-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 49–198（150 aa） Fragment：protein hedgehog N-product	Not recorded	PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；2.0M Na/K phosphate pH 6.4, 0.2M lithium sulfate, 0.05M CAPS pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.246
2IBG Crystal Structure of Hedgehog Bound to the FNIII Domains of Ihog Deposited 2006-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 49–198（150 aa） Fragment：protein hedgehog N-product	Not recorded	PO4 PHOSPHATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；2.0M Na/K phosphate pH 6.4, 0.2M lithium sulfate, 0.05M CAPS pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.246
2IBG Crystal Structure of Hedgehog Bound to the FNIII Domains of Ihog Deposited 2006-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 49–198（150 aa） Fragment：protein hedgehog N-product	Not recorded	PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；2.0M Na/K phosphate pH 6.4, 0.2M lithium sulfate, 0.05M CAPS pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.246
2IBG Crystal Structure of Hedgehog Bound to the FNIII Domains of Ihog Deposited 2006-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 49–198（150 aa） Fragment：protein hedgehog N-product	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；2.0M Na/K phosphate pH 6.4, 0.2M lithium sulfate, 0.05M CAPS pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.246
6TD6 Structure of Drosophila melanogaster Dispatched bound to a modified Hedgehog ligand, HhN-C85II Deposited 2019-11-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–471（471 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.76 Å

3 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HH_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–146； UniProt 258–403

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	6tyy
Deposition date deposition_date	2019-08-09
Structure title title	Hedgehog autoprocessing mutant D46H
Keywords keywords	Hedgehog autoprocessing doamin, SIGNALING PROTEIN; SIGNALING PROTEIN
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	15.70 Å
Radius of gyration Rg (electron density) rg_electron	14.39 Å
Forward intensity I(0) i0	4986930.00
Molecular weight molecular_weight	15981.0 kDa
Excluded volume excluded_volume	20035 Å³
Envelope volume envelope_volume	22348 Å³
Hydration-shell volume shell_volume	13103 Å³
Envelope diameter envelope_diameter	48.9 Å
Shell Rg shell_rg	20.27 Å
Envelope Rg envelope_rg	14.66 Å
Shape Rg shape_rg	14.37 Å
Total Rg total_rg	15.58 Å
Total atoms total_atoms	1122
Residues n_residues	145
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	50.1 Å
Rg (real space) rg_real	15.59 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	4.9870e+06
I(0) uncertainty (real space) i0_real_error	5.7760e+04
Rg (reciprocal space) rg_reciprocal	15.60 Å
I(0) (reciprocal space) i0_reciprocal	4987000.0000
Solution quality estimate total_estimate	0.7470
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.6 Å
Skewness Skewness skewness	0.131
Kurtosis Kurtosis kurtosis	-0.432
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1266000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 0.997; Smooth: 0.994

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6tyya_
Class class	b — All beta proteins
Fold Fold fold	b.86 — Hedgehog/intein (Hint) domain
Superfamily Superfamily superfamily	b.86.1 — Hedgehog/intein (Hint) domain
Family Family family	b.86.1.1 — Hedgehog C-terminal (Hog) autoprocessing domain

CATH v4.4 (1 domains)

Domain ID domain_id	6tyyA00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	16 — Endonuclease - Pi-scei; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Hedgehog/Intein (Hint) domain

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8. Citations (1)

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Unit-cell length a length_a	78.381 Å
Unit-cell length b length_b	78.381 Å
Unit-cell length c length_c	37.351 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	1.360 Å
Low-resolution limit resolution_low	25.656 Å
R factor r_factor	0.1722
R_work r_work	0.1705
R_free r_free	0.1949

Description description	Protein hedgehog
Molecular weight formula_weight	15999.3 kDa
Mutation mutation	D46H
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1309

Hedgehog autoprocessing mutant D46H

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

Protein hedgehog

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

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)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	161

fit	/app/data/saxs_computation/ty/6tyy/6tyy.fit
pddf	/app/data/pr_computation/ty/6tyy/6tyy.pr.out
profile	/app/data/saxs_computation/ty/6tyy/6tyy.dat