SAXSdb — 9d58

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

Dystrophin

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2–246	Fragment：actin-binding domain/calponin homology domains 1 and 2	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-Tris pH 6.7, 30% w/v Polyethylene monomethyl ether (MPEG) 5,000	Resolution 1.94 Å R-free 0.262
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 2–246	Fragment：actin-binding domain/calponin homology domains 1 and 2	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-Tris pH 6.7, 30% w/v Polyethylene monomethyl ether (MPEG) 5,000	Resolution 1.94 Å R-free 0.262
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 2–246	Fragment：actin-binding domain/calponin homology domains 1 and 2	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-Tris pH 6.7, 30% w/v Polyethylene monomethyl ether (MPEG) 5,000	Resolution 1.94 Å R-free 0.262
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 2–246	Fragment：actin-binding domain/calponin homology domains 1 and 2	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-Tris pH 6.7, 30% w/v Polyethylene monomethyl ether (MPEG) 5,000	Resolution 1.94 Å R-free 0.262

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 9D58	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DXX N-terminal Actin-binding Domain of Human Dystrophin Deposited 2000-01-20	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 1–246（246 aa） Fragment：ACTIN-BINDING Chain B 1–246（246 aa） Fragment：ACTIN-BINDING	Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；1.55M AMMONIUM FORMATE, 0.1M HEPES 7.4, pH 7.40	Resolution 2.60 Å R-free 0.268
1DXX N-terminal Actin-binding Domain of Human Dystrophin Deposited 2000-01-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–246（246 aa） Fragment：ACTIN-BINDING Chain D 1–246（246 aa） Fragment：ACTIN-BINDING	Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；1.55M AMMONIUM FORMATE, 0.1M HEPES 7.4, pH 7.40	Resolution 2.60 Å R-free 0.268
1EG3 STRUCTURE OF A DYSTROPHIN WW DOMAIN FRAGMENT IN COMPLEX WITH A BETA-DYSTROGLYCAN PEPTIDE Deposited 2000-02-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3046–3306（261 aa） Fragment：WW DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；ammonium sulfate, glycerol, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.00 Å R-free 0.257
1EG4 STRUCTURE OF A DYSTROPHIN WW DOMAIN FRAGMENT IN COMPLEX WITH A BETA-DYSTROGLYCAN PEPTIDE Deposited 2000-02-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 3046–3306（261 aa） Fragment：WW DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；ammonium sulfate, glycerol, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.249
3UUN Crystal Structure of N-terminal first spectrin repeat of dystrophin Deposited 2011-11-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 338–456（119 aa） Fragment：Spectrin Repeat, UNP residues 338-456	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294.15 K；0.1M Tris HCl, 2.0M Ammonium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K	Resolution 2.30 Å R-free 0.260
3UUN Crystal Structure of N-terminal first spectrin repeat of dystrophin Deposited 2011-11-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 338–456（119 aa） Fragment：Spectrin Repeat, UNP residues 338-456	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294.15 K；0.1M Tris HCl, 2.0M Ammonium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K	Resolution 2.30 Å R-free 0.260
3UUN Crystal Structure of N-terminal first spectrin repeat of dystrophin Deposited 2011-11-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 338–456（119 aa） Fragment：Spectrin Repeat, UNP residues 338-456 Chain B 338–456（119 aa） Fragment：Spectrin Repeat, UNP residues 338-456	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294.15 K；0.1M Tris HCl, 2.0M Ammonium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K	Resolution 2.30 Å R-free 0.260
9EC1 The Structure of Human Dystrophin Spectrin Repeat 24 Deposited 2024-11-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2933–3046（114 aa） Fragment：spectrin repeat 24	Not recorded	SO4 SULFATE ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Sodium citrate tribasic dihydrate, pH 5.6, 0.5 M Ammonium sulfate , 1 M Lithium sulfate monohydrate	Resolution 2.14 Å R-free 0.255
9EC1 The Structure of Human Dystrophin Spectrin Repeat 24 Deposited 2024-11-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2933–3046（114 aa） Fragment：spectrin repeat 24	Not recorded	SO4 SULFATE ION × 2 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Sodium citrate tribasic dihydrate, pH 5.6, 0.5 M Ammonium sulfate , 1 M Lithium sulfate monohydrate	Resolution 2.14 Å R-free 0.255
9EC1 The Structure of Human Dystrophin Spectrin Repeat 24 Deposited 2024-11-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2933–3046（114 aa） Fragment：spectrin repeat 24	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Sodium citrate tribasic dihydrate, pH 5.6, 0.5 M Ammonium sulfate , 1 M Lithium sulfate monohydrate	Resolution 2.14 Å R-free 0.255
9EC1 The Structure of Human Dystrophin Spectrin Repeat 24 Deposited 2024-11-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 2933–3046（114 aa） Fragment：spectrin repeat 24	Not recorded	SO4 SULFATE ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Sodium citrate tribasic dihydrate, pH 5.6, 0.5 M Ammonium sulfate , 1 M Lithium sulfate monohydrate	Resolution 2.14 Å R-free 0.255
9EC1 The Structure of Human Dystrophin Spectrin Repeat 24 Deposited 2024-11-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 2933–3046（114 aa） Fragment：spectrin repeat 24	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Sodium citrate tribasic dihydrate, pH 5.6, 0.5 M Ammonium sulfate , 1 M Lithium sulfate monohydrate	Resolution 2.14 Å R-free 0.255
9EC1 The Structure of Human Dystrophin Spectrin Repeat 24 Deposited 2024-11-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 2933–3046（114 aa） Fragment：spectrin repeat 24	Not recorded	SO4 SULFATE ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Sodium citrate tribasic dihydrate, pH 5.6, 0.5 M Ammonium sulfate , 1 M Lithium sulfate monohydrate	Resolution 2.14 Å R-free 0.255
9EC1 The Structure of Human Dystrophin Spectrin Repeat 24 Deposited 2024-11-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 2933–3046（114 aa） Fragment：spectrin repeat 24	Not recorded	SO4 SULFATE ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Sodium citrate tribasic dihydrate, pH 5.6, 0.5 M Ammonium sulfate , 1 M Lithium sulfate monohydrate	Resolution 2.14 Å R-free 0.255
9EC1 The Structure of Human Dystrophin Spectrin Repeat 24 Deposited 2024-11-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 2933–3046（114 aa） Fragment：spectrin repeat 24	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Sodium citrate tribasic dihydrate, pH 5.6, 0.5 M Ammonium sulfate , 1 M Lithium sulfate monohydrate	Resolution 2.14 Å R-free 0.255

5 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DMD_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–248； UniProt 2–246 Author chain B； PDBConstruct 4–248； UniProt 2–246 Author chain C； PDBConstruct 4–248； UniProt 2–246 Author chain D； PDBConstruct 4–248； UniProt 2–246

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	9d58
Deposition date deposition_date	2024-08-13
最后修订 last_revision	2025-03-12
Structure title title	Human Dystrophin tandem calponin homology actin-binding domain crystallized in a closed-state conformation
Keywords keywords	;Actin-binding domain, tandem calponin homology domain, Dystrophin, Duchenne Muscular Dystrophy, DMD, Cytoskeleton, STRUCTURAL PROTEIN ;; STRUCTURAL 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	33.74 Å
Radius of gyration Rg (electron density) rg_electron	32.62 Å
Forward intensity I(0) i0	160157000.00
Molecular weight molecular_weight	102170.0 kDa
Excluded volume excluded_volume	128530 Å³
Envelope volume envelope_volume	168810 Å³
Hydration-shell volume shell_volume	42943 Å³
Envelope diameter envelope_diameter	110.0 Å
Shell Rg shell_rg	39.77 Å
Envelope Rg envelope_rg	31.68 Å
Shape Rg shape_rg	32.63 Å
Total Rg total_rg	33.17 Å
Total atoms total_atoms	7230
Residues n_residues	926
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	102.0 Å
Rg (real space) rg_real	33.55 Å
Rg uncertainty (real space) rg_real_error	0.80 Å
I(0) (real space) i0_real	1.6020e+08
I(0) uncertainty (real space) i0_real_error	2.5150e+06
Rg (reciprocal space) rg_reciprocal	33.67 Å
I(0) (reciprocal space) i0_reciprocal	160200000.0000
Solution quality estimate total_estimate	0.9054
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	47.8 Å
Skewness Skewness skewness	0.053
Kurtosis Kurtosis kurtosis	-0.543
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	29250000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.942

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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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8. Citations (1)

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Unit-cell length a length_a	59.774 Å
Unit-cell length b length_b	143.138 Å
Unit-cell length c length_c	59.862 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.21 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	1.940 Å
Low-resolution limit resolution_low	58.510 Å
R factor r_factor	0.2407
R_work r_work	0.2157
R_free r_free	0.2617

Description description	Dystrophin
Molecular weight formula_weight	28573.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7475

Human Dystrophin tandem calponin homology actin-binding domain crystallized in a closed-state conformation

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

Dystrophin

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	239

fit	/app/data/saxs_computation/d5/9d58/9d58.fit
pddf	/app/data/pr_computation/d5/9d58/9d58.pr.out
profile	/app/data/saxs_computation/d5/9d58/9d58.dat