SAXSdb — 5fw9

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

SPECTRIN ALPHA CHAIN, NON-ERYTHROCYTIC 1

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 965–1025	Fragment：SH3 DOMAIN, RESIDUES 965-1025 Mutation：YES	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.55 Å R-free 0.249

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 5FW9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2FOT Crystal structure of the complex between calmodulin and alphaII-spectrin Deposited 2006-01-13	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 C 1172–1211（40 aa） Fragment：Calmodulin binding domain	Mutation：L1211R	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；50mM Tris,pH 8.00, 30% PEG 8000, 0.1M ammonium-sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.45 Å R-free 0.269
3F31 Crystal Structure of the N-terminal region of AlphaII-spectrin Tetramerization Domain Deposited 2008-10-30	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 1–147（147 aa） Chain B 1–147（147 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；PEG8000:PEG1000 (1:2), 4% 1,4-butane-diol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.280
3F31 Crystal Structure of the N-terminal region of AlphaII-spectrin Tetramerization Domain Deposited 2008-10-30	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–147（147 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；PEG8000:PEG1000 (1:2), 4% 1,4-butane-diol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.280
3F31 Crystal Structure of the N-terminal region of AlphaII-spectrin Tetramerization Domain Deposited 2008-10-30	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–147（147 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；PEG8000:PEG1000 (1:2), 4% 1,4-butane-diol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.280
3FB2 Crystal structure of the human brain alpha spectrin repeats 15 and 16. Northeast Structural Genomics Consortium target HR5563a. Deposited 2008-11-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1337–1544（208 aa） Fragment：Repeats 15 and 16	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions microbatch crystallization under oil；pH 5；277 K；12% PEG 20000, 0.1M magnesium sulfate, 0.1M sodium acetate, pH 5.0, microbatch crystallization under oil, temperature 277K	Resolution 2.30 Å R-free 0.248
3FB2 Crystal structure of the human brain alpha spectrin repeats 15 and 16. Northeast Structural Genomics Consortium target HR5563a. Deposited 2008-11-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1337–1544（208 aa） Fragment：Repeats 15 and 16	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions microbatch crystallization under oil；pH 5；277 K；12% PEG 20000, 0.1M magnesium sulfate, 0.1M sodium acetate, pH 5.0, microbatch crystallization under oil, temperature 277K	Resolution 2.30 Å R-free 0.248
5FWB Human Spectrin SH3 domain D48G, E7F, K60F Deposited 2016-02-12	Different construct Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 965–1022（58 aa） Fragment：SH3, UNP RESIDUES 965-1025	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.50 Å R-free 0.236
5FWC Human Spectrin SH3 domain D48G, E7A, K60A Deposited 2016-02-12	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 965–1022（58 aa） Fragment：SH3, RESIDUES 965-1022	Mutation：YES	EDO 1,2-ETHANEDIOL × 2 NH4 AMMONIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.40 Å R-free 0.238
6ZEH Structure of PP1-spectrin alpha II chimera [PP1(7-304) + linker (G/S)x9 + spectrin alpha II (1025-1039)] bound to Phactr1 (516-580) Deposited 2020-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1025–1039（15 aa）	Mutation：N-terminal Vector derived sequence GHMGS	MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20% (w/v) polyethylene glycol 3350, 0.2 M NaI and 0.1 M BIS-Tris propane pH 8.5	Resolution 1.30 Å R-free 0.169
6ZEH Structure of PP1-spectrin alpha II chimera [PP1(7-304) + linker (G/S)x9 + spectrin alpha II (1025-1039)] bound to Phactr1 (516-580) Deposited 2020-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1025–1039（15 aa）	Mutation：N-terminal Vector derived sequence GHMGS	MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20% (w/v) polyethylene glycol 3350, 0.2 M NaI and 0.1 M BIS-Tris propane pH 8.5	Resolution 1.30 Å R-free 0.169

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

View Construct and Data Evidence

UniProt name	SPTN1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–62； UniProt 965–1025

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	5fw9
Deposition date deposition_date	2016-02-12
Structure title title	Human Spectrin SH3 domain D48G, E7Y, K60Y
Keywords keywords	SPECTRIN, SPECTRIN SH3, 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	11.91 Å
Radius of gyration Rg (electron density) rg_electron	10.42 Å
Forward intensity I(0) i0	940981.00
Molecular weight molecular_weight	6682.0 kDa
Excluded volume excluded_volume	8555 Å³
Envelope volume envelope_volume	9256 Å³
Hydration-shell volume shell_volume	7747 Å³
Envelope diameter envelope_diameter	35.6 Å
Shell Rg shell_rg	15.85 Å
Envelope Rg envelope_rg	10.84 Å
Shape Rg shape_rg	10.38 Å
Total Rg total_rg	12.16 Å
Total atoms total_atoms	473
Residues n_residues	57
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	38.7 Å
Rg (real space) rg_real	11.84 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	9.4100e+05
I(0) uncertainty (real space) i0_real_error	9.6990e+03
Rg (reciprocal space) rg_reciprocal	11.84 Å
I(0) (reciprocal space) i0_reciprocal	941000.0000
Solution quality estimate total_estimate	0.8718
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.7 Å
Skewness Skewness skewness	0.163
Kurtosis Kurtosis kurtosis	-0.218
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	298700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.796; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.946

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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	d5fw9a_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.1 — SH3-domain

CATH v4.4 (1 domains)

Domain ID domain_id	5fw9A00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

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8. Citations (1)

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Unit-cell length a length_a	33.234 Å
Unit-cell length b length_b	42.005 Å
Unit-cell length c length_c	50.336 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	1.550 Å
Low-resolution limit resolution_low	32.250 Å
R factor r_factor	0.2052
R_work r_work	0.2032
R_free r_free	0.2489

Description description	SPECTRIN ALPHA CHAIN, NON-ERYTHROCYTIC 1
Molecular weight formula_weight	7239.3 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	545

Human Spectrin SH3 domain D48G, E7Y, K60Y

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

SPECTRIN ALPHA CHAIN, NON-ERYTHROCYTIC 1

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	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	65

fit	/app/data/saxs_computation/fw/5fw9/5fw9.fit
pddf	/app/data/pr_computation/fw/5fw9/5fw9.pr.out
profile	/app/data/saxs_computation/fw/5fw9/5fw9.dat