SAXSdb — 3edu

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

Spectrin beta chain, erythrocyte

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 1692–1907	Fragment：Spectrin 14-Spectrin 15 di-repeat	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.2；289 K；0.1M bis-tris-propane, pH 6.2, 0.2M KSCN, 20% PEG 3,350, 3-10mM spermine, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.10 Å R-free 0.252

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 3EDU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1S35 Crystal Structure of Repeats 8 and 9 of Human Erythroid Spectrin Deposited 2004-01-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1063–1275（213 aa） Fragment：repeats 8 and 9	Mutation：L1063E	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M Sodium Citrate, 0.3 M Ammonium Sulfate, 1.2-1.3 M Lithium Sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.40 Å R-free 0.259
3F57 Crystal structure of human erythroid beta spectrin repeats 14 and 15 (ankyrin binding domain) Deposited 2008-11-03	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1686–1907（222 aa） Fragment：HUMAN ERYTHROID BETA SPECTRIN REPEATS 14 AND 15 (ANKYRIN BINDING DOMAIN): UNP RESIDUES 1686-1907	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；30% PEG 3350, 0.2 M NaCl, 100 mM Tris-HCl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.90 Å R-free 0.322
3F57 Crystal structure of human erythroid beta spectrin repeats 14 and 15 (ankyrin binding domain) Deposited 2008-11-03	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1686–1907（222 aa） Fragment：HUMAN ERYTHROID BETA SPECTRIN REPEATS 14 AND 15 (ANKYRIN BINDING DOMAIN): UNP RESIDUES 1686-1907	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；30% PEG 3350, 0.2 M NaCl, 100 mM Tris-HCl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.90 Å R-free 0.322
3KBT Crystal structure of the ankyrin binding domain of human erythroid beta spectrin (repeats 13-15) in complex with the spectrin binding domain of human erythroid ankyrin (ZU5-ANK) Deposited 2009-10-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1583–1906（324 aa） Fragment：UNP residues 1583-1906	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；Protein complex at 7.5 mg/mL mixed 1:1 with 0.05 M MES pH 6.5, 0.2 M ammonium acetate, 0.01 M calcium chloride, 10% PEG-4000, 5 mM dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.75 Å R-free 0.292
3KBT Crystal structure of the ankyrin binding domain of human erythroid beta spectrin (repeats 13-15) in complex with the spectrin binding domain of human erythroid ankyrin (ZU5-ANK) Deposited 2009-10-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1583–1906（324 aa） Fragment：UNP residues 1583-1906	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；Protein complex at 7.5 mg/mL mixed 1:1 with 0.05 M MES pH 6.5, 0.2 M ammonium acetate, 0.01 M calcium chloride, 10% PEG-4000, 5 mM dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.75 Å R-free 0.292
3KBU Crystal structure of the ankyrin binding domain of human erythroid beta spectrin (repeats 13-15) in complex with the spectrin binding domain of human erythroid ankyrin (ZU5-ANK), EMTS derivative Deposited 2009-10-20	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 A 1583–1906（324 aa） Fragment：UNP residues 1583-1906	Mutation：E1680C	HG MERCURY (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；Protein complex at 7.5 mg/mL mixed 1:1 with 0.05 M MES pH 6.5, 0.2 M ammonium acetate, 0.01 M calcium chloride, 10% PEG-4000, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.75 Å R-free 0.277
3KBU Crystal structure of the ankyrin binding domain of human erythroid beta spectrin (repeats 13-15) in complex with the spectrin binding domain of human erythroid ankyrin (ZU5-ANK), EMTS derivative Deposited 2009-10-20	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 B 1583–1906（324 aa） Fragment：UNP residues 1583-1906	Mutation：E1680C	HG MERCURY (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；Protein complex at 7.5 mg/mL mixed 1:1 with 0.05 M MES pH 6.5, 0.2 M ammonium acetate, 0.01 M calcium chloride, 10% PEG-4000, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.75 Å R-free 0.277
3LBX Crystal Structure of the Erythrocyte Spectrin Tetramerization Domain Complex Deposited 2010-01-08	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1902–2084（183 aa） Fragment：UNP residues 1902-2084	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M MES pH 6.5, 10% PEG-6000, 10% glycerol, 5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.299

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SPTB1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–218； UniProt 1692–1907

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	3edu
Deposition date deposition_date	2008-09-03
Structure title title	Crystal structure of the ankyrin-binding domain of human erythroid spectrin
Keywords keywords	;spectrin, ankyrin, ankyrin-binding domain, Actin capping, Actin-binding, Cytoskeleton, Disease mutation, Elliptocytosis, Hereditary hemolytic anemia, Phosphoprotein, 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	26.22 Å
Radius of gyration Rg (electron density) rg_electron	26.56 Å
Forward intensity I(0) i0	8211750.00
Molecular weight molecular_weight	21223.0 kDa
Excluded volume excluded_volume	26410 Å³
Envelope volume envelope_volume	34127 Å³
Hydration-shell volume shell_volume	12994 Å³
Envelope diameter envelope_diameter	95.5 Å
Shell Rg shell_rg	28.50 Å
Envelope Rg envelope_rg	27.02 Å
Shape Rg shape_rg	26.57 Å
Total Rg total_rg	26.79 Å
Total atoms total_atoms	1499
Residues n_residues	191
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	95.4 Å
Rg (real space) rg_real	26.79 Å
Rg uncertainty (real space) rg_real_error	1.10 Å
I(0) (real space) i0_real	8.2120e+06
I(0) uncertainty (real space) i0_real_error	1.2280e+05
Rg (reciprocal space) rg_reciprocal	26.61 Å
I(0) (reciprocal space) i0_reciprocal	8211000.0000
Solution quality estimate total_estimate	0.6903
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.2 Å
Skewness Skewness skewness	0.637
Kurtosis Kurtosis kurtosis	-0.381
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	996600.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.324; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.070; Smooth: 0.926

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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) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3eduA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	60 —

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8. Citations (1)

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Unit-cell length a length_a	74.823 Å
Unit-cell length b length_b	111.746 Å
Unit-cell length c length_c	127.734 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	16

Space group space_group	F 2 2 2
Space-group number int_tables_number	22
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	31.000 Å
R factor r_factor	0.2148
R_work r_work	0.2103
R_free r_free	0.2518

Description description	Spectrin beta chain, erythrocyte
Molecular weight formula_weight	24810.5 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	1667

Crystal structure of the ankyrin-binding domain of human erythroid spectrin

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

Spectrin beta chain, erythrocyte

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

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) 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	136

fit	/app/data/saxs_computation/ed/3edu/3edu.fit
pddf	/app/data/pr_computation/ed/3edu/3edu.pr.out
profile	/app/data/saxs_computation/ed/3edu/3edu.dat