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8bwa

Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1) in complex with platinum

Method: X-RAY DIFFRACTION Dmax: 76.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Twisted gastrulation protein homolog 1

Homo sapiens

UniProt Q9GZX9

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 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
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 26–223 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

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 8BWA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 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 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
8BWI Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1), crystal form 2 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 No recorded non-water small molecule 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
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 6 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 Author chain B； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 8bwa

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8bwa
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8bwa
Deposition date deposition_date2022-12-06
Structure title titleCrystal structure of human Twisted gastrulation protein homolog 1 (TWSG1) in complex with platinum
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 methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.13 Å
Radius of gyration Rg (electron density) rg_electron26.24 Å
Forward intensity I(0) i031643200.00
Molecular weight molecular_weight37709.0 kDa
Excluded volume excluded_volume44349 ų
Envelope volume envelope_volume63263 ų
Hydration-shell volume shell_volume21102 ų
Envelope diameter envelope_diameter78.9 Å
Shell Rg shell_rg32.15 Å
Envelope Rg envelope_rg25.48 Å
Shape Rg shape_rg26.15 Å
Total Rg total_rg27.12 Å
Total atoms total_atoms4813
Residues n_residues328
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax76.5 Å
Rg (real space) rg_real26.93 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real3.1640e+07
I(0) uncertainty (real space) i0_real_error4.1460e+05
Rg (reciprocal space) rg_reciprocal27.00 Å
I(0) (reciprocal space) i0_reciprocal31640000.0000
Solution quality estimate total_estimate0.8875
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary42.2 Å
Skewness Skewness skewness-0.147
Kurtosis Kurtosis kurtosis-0.805
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1914000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.877
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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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8. Citations (1)

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9. Files and Curves (10)