SAXSdb — 8bwi

▼

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

Twisted gastrulation protein homolog 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 26–223	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；294 K；1.0 M K/Na tartrate, 0.1 M MES pH 6.0	Resolution 3.40 Å R-free 0.342

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 8BWI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8BWA Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1) in complex with platinum Deposited 2022-12-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–223（198 aa）	Not recorded	PT PLATINUM (II) ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.77 M LiCl, 15.5% w/v PEG 6000, 77 mM HEPES pH 7.0, 5.2% 2,2,2-trifluoroethanol. The crystal was soaked in saturated solution of di-mu-iodobis(ethylenediamine)diplatinum(2) nitrate (PIP) solution before data collection.	Resolution 3.61 Å R-free 0.390
8BWA Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1) in complex with platinum Deposited 2022-12-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 26–223（198 aa）	Not recorded	PT PLATINUM (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.77 M LiCl, 15.5% w/v PEG 6000, 77 mM HEPES pH 7.0, 5.2% 2,2,2-trifluoroethanol. The crystal was soaked in saturated solution of di-mu-iodobis(ethylenediamine)diplatinum(2) nitrate (PIP) solution before data collection.	Resolution 3.61 Å R-free 0.390
8BWD Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1), crystal form 1 Deposited 2022-12-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–223（198 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.85 M LiCl, 17.1% w/v PEG 6000, 85 mM HEPES pH 7.0, 3.6% 1,1,1,3,3,3-hexafluoro-2-propanol	Resolution 2.63 Å R-free 0.305
8BWD Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1), crystal form 1 Deposited 2022-12-06	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 26–223（198 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.85 M LiCl, 17.1% w/v PEG 6000, 85 mM HEPES pH 7.0, 3.6% 1,1,1,3,3,3-hexafluoro-2-propanol	Resolution 2.63 Å R-free 0.305
8BWL Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1) in complex with human Growth Differentiation factor 5 (GDF5) and calcium Deposited 2022-12-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 26–83（58 aa） Chain D 26–83（58 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；12.1% w/v PEG 1000, 12.1% w/v PEG 3350, 12.1% v/v MPD, 97 mM CaCl2, 0.097 M Bicine/Trizma pH 8.5	Resolution 1.96 Å R-free 0.212
8BWM Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1) in complex with human Growth Differentiation factor 5 (GDF5) and calcium, long-wavelength X-ray dataset (4042 eV) Deposited 2022-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 26–83（58 aa） Chain D 26–83（58 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；12.1% w/v PEG 1000, 12.1% w/v PEG 3350, 12.1% v/v MPD, 97 mM CaCl2, 0.097 M Bicine/Trizma pH 8.5	Resolution 2.50 Å R-free 0.278
8BWN Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1) in complex with human Growth Differentiation Factor 5 (GDF5) and calcium, long-wavelength X-ray dataset (4010 eV) Deposited 2022-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 26–83（58 aa） Chain D 26–83（58 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 100 mM CaCl2, 0.1 M MOPS/HEPES-Na pH 7.5	Resolution 2.57 Å R-free 0.283

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TWSG1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–201； UniProt 26–223

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	8bwi
Deposition date deposition_date	2022-12-06
Structure title title	Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1), crystal form 2
Keywords keywords	;Twisted gastrulation protein homolog 1 (TWSG1), Transforming Growth Factor beta (TGF-beta) signalling pathway, extracellular protein, disulfide rich domains., SIGNALING PROTEIN ;; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	23.02 Å
Radius of gyration Rg (electron density) rg_electron	22.71 Å
Forward intensity I(0) i0	7258660.00
Molecular weight molecular_weight	18438.0 kDa
Excluded volume excluded_volume	22363 Å³
Envelope volume envelope_volume	31169 Å³
Hydration-shell volume shell_volume	12896 Å³
Envelope diameter envelope_diameter	77.8 Å
Shell Rg shell_rg	26.66 Å
Envelope Rg envelope_rg	22.17 Å
Shape Rg shape_rg	22.65 Å
Total Rg total_rg	23.43 Å
Total atoms total_atoms	2442
Residues n_residues	166
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	80.2 Å
Rg (real space) rg_real	23.24 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	7.2590e+06
I(0) uncertainty (real space) i0_real_error	1.0410e+05
Rg (reciprocal space) rg_reciprocal	23.19 Å
I(0) (reciprocal space) i0_reciprocal	7258000.0000
Solution quality estimate total_estimate	0.5063
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	16.0 Å
Skewness Skewness skewness	0.338
Kurtosis Kurtosis kurtosis	-0.935
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	932500.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.285; Stabil: 1.000; Sysdev: 0.171; Positv: 1.000; Valcen: 0.210; Smooth: 1.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▶

8. Citations (1)

▶

Unit-cell length a length_a	92.250 Å
Unit-cell length b length_b	92.250 Å
Unit-cell length c length_c	95.960 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	12

Space group space_group	P 64 2 2
Space-group number int_tables_number	181
Crystal system crystal_system	hexagonal

Resolution resolution	3.400 Å
Low-resolution limit resolution_low	46.120 Å
R factor r_factor	0.2977
R_work r_work	0.2955
R_free r_free	0.3424

Description description	Twisted gastrulation protein homolog 1
Molecular weight formula_weight	23569.8 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	2442

Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1), crystal form 2

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

Twisted gastrulation protein homolog 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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

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	Homo sapiens

fit	/app/data/saxs_computation/bw/8bwi/8bwi.fit
pddf	/app/data/pr_computation/bw/8bwi/8bwi.pr.out
profile	/app/data/saxs_computation/bw/8bwi/8bwi.dat