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Yorodumi- PDB-8bwd: Crystal structure of human Twisted gastrulation protein homolog 1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bwd | |||||||||||||||
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Title | Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1), crystal form 1 | |||||||||||||||
Components | Twisted gastrulation protein homolog 1 | |||||||||||||||
Keywords | SIGNALING PROTEIN / Twisted gastrulation protein homolog 1 (TWSG1) / Transforming Growth Factor beta (TGF-beta) signalling pathway / extracellular protein / disulfide rich domains. | |||||||||||||||
Function / homology | Function and homology information 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 BMP signaling pathway / negative regulation of cytokine production / negative regulation of osteoblast differentiation / BMP signaling pathway ...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 BMP signaling pathway / negative regulation of cytokine production / negative regulation of osteoblast differentiation / BMP signaling pathway / salivary gland morphogenesis / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of SMAD protein signal transduction / hemopoiesis / mesoderm formation / chondrocyte differentiation / ossification / forebrain development / heparin binding / extracellular space Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å | |||||||||||||||
Authors | 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 | United Kingdom, European Union, France, 4items
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Citation | Journal: Nat Commun / Year: 2024 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bwd.cif.gz | 230.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bwd.ent.gz | 157.6 KB | Display | PDB format |
PDBx/mmJSON format | 8bwd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bwd_validation.pdf.gz | 452.6 KB | Display | wwPDB validaton report |
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Full document | 8bwd_full_validation.pdf.gz | 457 KB | Display | |
Data in XML | 8bwd_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 8bwd_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/8bwd ftp://data.pdbj.org/pub/pdb/validation_reports/bw/8bwd | HTTPS FTP |
-Related structure data
Related structure data | 8bwaC 8bwiC 8bwlC 8bwmC 8bwnC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.999750586203, -0.0213452496622, -0.00656853894213), (0.0222644448252, -0.975632324304, -0.218279321672), (-0.0017492522982, -0.218371124671, 0.975864228275)Vector: - ...NCS oper: (Code: given Matrix: (-0.999750586203, -0.0213452496622, -0.00656853894213), Vector: |
-Components
#1: Protein | Mass: 23569.760 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TWSG1, TSG, PSEC0250 / Cell line (production host): HEK293T / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: Q9GZX9 #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.41 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 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 PH range: 7.0-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.627→84.864 Å / Num. obs: 8855 / % possible obs: 53 % / Redundancy: 18.8 % / Biso Wilson estimate: 82.65 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.019 / Rrim(I) all: 0.08 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.627→2.999 Å / Rmerge(I) obs: 1.603 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 443 / Rpim(I) all: 0.377 / Rrim(I) all: 1.648 / % possible all: 8.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→42.43 Å / SU ML: 0.3495 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.4611 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 100.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.63→42.43 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.608144477686 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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