SAXSdb — 5j4o

▼

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

Spectrin alpha chain, 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 1599–1826	Fragment：UNP residues 1599-1826	EDO 1,2-ETHANEDIOL × 4 PG4 TETRAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Molecular Dimensions Morpheus crystallisation screen, condition A2: 0.03M MgCl2, 0.03M CaCl2, 0.1M MES/Imidazole pH 6.5, 20% v/v Ethylene glycol, 10% v/v PEG 8000.	Resolution 1.54 Å R-free 0.229

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 5J4O	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1OWA Solution Structural Studies on Human Erythrocyte Alpha Spectrin N Terminal Tetramerization Domain Deposited 2003-03-28	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–156（156 aa） Fragment：residues 1-156	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；293 K；Ionic strength (raw mmCIF value) 5mM Phosphate, 150mM NaCl；Pressure ambient NMR sample composition 1mM spectrin, 5mM Phosphate, 150mM NaCl, 5% D2O, 95 % H2O \| 5% D2O, 95 % H2O	Resolution not provided
3LBX Crystal Structure of the Erythrocyte Spectrin Tetramerization Domain Complex Deposited 2010-01-08	Different construct 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 1–158（158 aa）	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

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SPTA1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–231； UniProt 1599–1826

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5j4o
Deposition date deposition_date	2016-04-01
Structure title title	Structure of human erythrocytic Spectrin alpha chain repeats 16-17
Keywords keywords	erythrocyte, spectrin, helical bundle, domains, structural protein; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	31.00 Å
Radius of gyration Rg (electron density) rg_electron	31.68 Å
Forward intensity I(0) i0	11770200.00
Molecular weight molecular_weight	26253.0 kDa
Excluded volume excluded_volume	32904 Å³
Envelope volume envelope_volume	45658 Å³
Hydration-shell volume shell_volume	14646 Å³
Envelope diameter envelope_diameter	115.8 Å
Shell Rg shell_rg	31.17 Å
Envelope Rg envelope_rg	32.32 Å
Shape Rg shape_rg	31.65 Å
Total Rg total_rg	31.72 Å
Total atoms total_atoms	3671
Residues n_residues	222
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	117.2 Å
Rg (real space) rg_real	31.81 Å
Rg uncertainty (real space) rg_real_error	1.56 Å
I(0) (real space) i0_real	1.1770e+07
I(0) uncertainty (real space) i0_real_error	2.2030e+05
Rg (reciprocal space) rg_reciprocal	31.47 Å
I(0) (reciprocal space) i0_reciprocal	11770000.0000
Solution quality estimate total_estimate	0.6377
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	18.4 Å
Skewness Skewness skewness	0.653
Kurtosis Kurtosis kurtosis	-0.383
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	813600.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.126; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.013; Smooth: 0.896

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Spectrin alpha chain, erythrocytic 1
Molecular weight formula_weight	26757.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4074

GPGKGKKLNEASRQQRFNTSIRDFEFWLSEAETLLAMKDQARDLASAGNLLKKHQLLEREMLAREDALKDLNTLAEDLLSSGTFNVDQIVKKKDNVNKRFLNVQELAAAHHEKLKEAYALFQFFQDLDDEESWIEEKLIRVSSQDYGRDLQGVQNLLKKHKRLEGELVAHEPAIQNVLDMAEKLKDKAAVGQEEIQLRLAQFVEHWEKLKELAKARGLKLEESLEYLQFMQ

来源 Source

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	250

▼

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5j4oa1
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.1 — Spectrin repeat
Family Family family	a.7.1.0 — automated matches

Domain ID domain_id	d5j4oa2
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.1 — Spectrin repeat
Family Family family	a.7.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	5j4oA01
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 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	37.640 Å
Unit-cell length b length_b	43.670 Å
Unit-cell length c length_c	154.280 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	1.540 Å
Low-resolution limit resolution_low	30.180 Å
R factor r_factor	0.2099
R_work r_work	0.2090
R_free r_free	0.2290

fit	/app/data/saxs_computation/j4/5j4o/5j4o.fit
pddf	/app/data/pr_computation/j4/5j4o/5j4o.pr.out
profile	/app/data/saxs_computation/j4/5j4o/5j4o.dat

Structure of human erythrocytic Spectrin alpha chain repeats 16-17

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

Spectrin alpha chain, 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