[English] 日本語
![](img/lk-miru.gif)
- PDB-8bwa: Crystal structure of human Twisted gastrulation protein homolog 1... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8bwa | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1) in complex with platinum | |||||||||||||||
![]() | Twisted gastrulation protein homolog 1 | |||||||||||||||
![]() | SIGNALING PROTEIN / Twisted gastrulation protein homolog 1 (TWSG1) / Transforming Growth Factor beta (TGF-beta) signalling pathway / extracellular protein / disulfide rich domains. | |||||||||||||||
Function / homology | ![]() negative regulation of CD4-positive, alpha-beta T cell activation / regulation of BMP signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of BMP signaling pathway / transforming growth factor beta binding / camera-type eye development / negative regulation of cytokine production / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of SMAD protein signal transduction / hemopoiesis ...negative regulation of CD4-positive, alpha-beta T cell activation / regulation of BMP signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of BMP signaling pathway / transforming growth factor beta binding / camera-type eye development / negative regulation of cytokine production / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of SMAD protein signal transduction / hemopoiesis / mesoderm formation / negative regulation of BMP signaling pathway / negative regulation of osteoblast differentiation / chondrocyte differentiation / BMP signaling pathway / salivary gland morphogenesis / forebrain development / ossification / heparin binding / extracellular space Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Malinauskas, T. / Rudolf, A.F. / Moore, G. / Eggington, H. / Belnoue-Davis, H. / El Omari, K. / Woolley, R.E. / Griffiths, S.C. / Duman, R. / Wagner, A. ...Malinauskas, T. / Rudolf, A.F. / Moore, G. / Eggington, H. / Belnoue-Davis, H. / El Omari, K. / Woolley, R.E. / Griffiths, S.C. / Duman, R. / Wagner, A. / Leedham, S.J. / Baldock, C. / Ashe, H. / Siebold, C. | |||||||||||||||
Funding support | ![]() ![]()
| |||||||||||||||
![]() | ![]() Title: Molecular mechanism of BMP signal control by Twisted gastrulation. Authors: Malinauskas, T. / Moore, G. / Rudolf, A.F. / Eggington, H. / Belnoue-Davis, H.L. / El Omari, K. / Griffiths, S.C. / Woolley, R.E. / Duman, R. / Wagner, A. / Leedham, S.J. / Baldock, C. / Ashe, H.L. / Siebold, C. | |||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 230.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 160.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 448.9 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 16.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bwdC ![]() 8bwiC ![]() 8bwlC ![]() 8bwmC ![]() 8bwnC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.999810319277, -0.018725413673, -0.0053557772176), (0.0194310789822, -0.977757879793, -0.208834771225), (-0.00132613589644, -0.208899227824, 0.977936272964)Vector: - ...NCS oper: (Code: given Matrix: (-0.999810319277, -0.018725413673, -0.0053557772176), Vector: |
-
Components
#1: Protein | Mass: 23569.760 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Protein crystals were soaked with Di-mu-iodobis(ethylenediamine)diplatinum(2) nitrate (PIP) for phasing. Source: (gene. exp.) ![]() ![]() #2: Chemical | ChemComp-PT / Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.93 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 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) ...Details: 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. PH range: 7.0-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 31, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03003 Å / Relative weight: 1 |
Reflection | Resolution: 3.61→62.72 Å / Num. obs: 6653 / % possible obs: 99.5 % / Redundancy: 25.8 % / Biso Wilson estimate: 202.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.029 / Rrim(I) all: 0.146 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 3.61→3.67 Å / Redundancy: 25.4 % / Rmerge(I) obs: 7.612 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 319 / CC1/2: 0.247 / Rpim(I) all: 1.524 / Rrim(I) all: 7.767 / % possible all: 99.7 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 245.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.61→49.22 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.214171879878 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
|