SAXSdb — 8x8k

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

Starch-binding domain-containing protein 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	Other combination Monomer Protein × 1 其他Polymer 2 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 260–358	Fragment：CBM20 domain	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.09 M Halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M Buffer System 1 (Imidazole; MES (acid) pH 6.5), 37.5% v/v Precipitant Mix 4 (25% v/v MPD (racemic); 25% PEG 1000; 25% w/v PEG 3350)	Resolution 2.10 Å R-free 0.226
2	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 260–358	Fragment：CBM20 domain	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.09 M Halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M Buffer System 1 (Imidazole; MES (acid) pH 6.5), 37.5% v/v Precipitant Mix 4 (25% v/v MPD (racemic); 25% PEG 1000; 25% w/v PEG 3350)	Resolution 2.10 Å R-free 0.226
3	Other combination Monomer Protein × 1 其他Polymer 2 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 260–358	Fragment：CBM20 domain	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.09 M Halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M Buffer System 1 (Imidazole; MES (acid) pH 6.5), 37.5% v/v Precipitant Mix 4 (25% v/v MPD (racemic); 25% PEG 1000; 25% w/v PEG 3350)	Resolution 2.10 Å R-free 0.226
4	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 260–358	Fragment：CBM20 domain	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.09 M Halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M Buffer System 1 (Imidazole; MES (acid) pH 6.5), 37.5% v/v Precipitant Mix 4 (25% v/v MPD (racemic); 25% PEG 1000; 25% w/v PEG 3350)	Resolution 2.10 Å R-free 0.226

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 8X8K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8X8A Crystal structure of STBD1 LIR motif in complex with GABARAPL1 Deposited 2023-11-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 200–210（11 aa） Fragment：LIR motif	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；25% w/v Pentaerythritol Propoxylate (5/4 PO/OH), 0.1 M Sodium acetate pH 4.6, 0.05 M Magnesium chloride	Resolution 1.53 Å R-free 0.187

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	STBD1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–99； UniProt 260–358 Author chain B； PDBConstruct 1–99； UniProt 260–358 Author chain C； PDBConstruct 1–99； UniProt 260–358 Author chain D； PDBConstruct 1–99； UniProt 260–358

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	8x8k
Deposition date deposition_date	2023-11-27
最后修订 last_revision	2024-09-18
Structure title title	Crystal structure of STBD1 CBM20 domain in complex with maltotetraose
Keywords keywords	STBD1, CBM20, maltotetraose, PROTEIN BINDING; PROTEIN BINDING
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	25.77 Å
Radius of gyration Rg (electron density) rg_electron	24.81 Å
Forward intensity I(0) i0	40387000.00
Molecular weight molecular_weight	49070.0 kDa
Excluded volume excluded_volume	61199 Å³
Envelope volume envelope_volume	76748 Å³
Hydration-shell volume shell_volume	26299 Å³
Envelope diameter envelope_diameter	81.2 Å
Shell Rg shell_rg	31.59 Å
Envelope Rg envelope_rg	24.65 Å
Shape Rg shape_rg	24.78 Å
Total Rg total_rg	25.68 Å
Total atoms total_atoms	3476
Residues n_residues	389
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	78.7 Å
Rg (real space) rg_real	25.69 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	4.0390e+07
I(0) uncertainty (real space) i0_real_error	5.4160e+05
Rg (reciprocal space) rg_reciprocal	25.72 Å
I(0) (reciprocal space) i0_reciprocal	40390000.0000
Solution quality estimate total_estimate	0.9148
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.0 Å
Skewness Skewness skewness	0.197
Kurtosis Kurtosis kurtosis	-0.540
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8743000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.972; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.972

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Starch-binding domain-containing protein 1
Molecular weight formula_weight	11546.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3589

GSQQVSVRFQVHYVTSTDVQFIAVTGDHECLGRWNTYIPLHYNKDGFWSHSIFLPADTVVEWKFVLVENGGVTRWEECSNRFLETGHEDKVVHAWWGIH

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

Entity 2 Entity 2 branched

Description description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
Molecular weight formula_weight	666.6 kDa
Source method src_method	man
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	113

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8. Citations (1)

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Unit-cell length a length_a	74.879 Å
Unit-cell length b length_b	74.879 Å
Unit-cell length c length_c	163.087 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	24

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	trigonal

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	41.660 Å
R factor r_factor	0.1885
R_work r_work	0.1865
R_free r_free	0.2263

fit	/app/data/saxs_computation/x8/8x8k/8x8k.fit
pddf	/app/data/pr_computation/x8/8x8k/8x8k.pr.out
profile	/app/data/saxs_computation/x8/8x8k/8x8k.dat

Crystal structure of STBD1 CBM20 domain in complex with maltotetraose

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

Starch-binding domain-containing protein 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