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Yorodumi- PDB-1tgj: HUMAN TRANSFORMING GROWTH FACTOR-BETA 3, CRYSTALLIZED FROM DIOXANE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tgj | |||||||||
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Title | HUMAN TRANSFORMING GROWTH FACTOR-BETA 3, CRYSTALLIZED FROM DIOXANE | |||||||||
Components | TRANSFORMING GROWTH FACTOR-BETA 3Transforming growth factor beta | |||||||||
Keywords | GROWTH FACTOR / MITOGEN / GLYCOPROTEIN | |||||||||
Function / homology | Function and homology information frontal suture morphogenesis / uterine wall breakdown / detection of hypoxia / embryonic neurocranium morphogenesis / type III transforming growth factor beta receptor binding / positive regulation of tight junction disassembly / negative regulation of macrophage cytokine production / secondary palate development / response to laminar fluid shear stress / type II transforming growth factor beta receptor binding ...frontal suture morphogenesis / uterine wall breakdown / detection of hypoxia / embryonic neurocranium morphogenesis / type III transforming growth factor beta receptor binding / positive regulation of tight junction disassembly / negative regulation of macrophage cytokine production / secondary palate development / response to laminar fluid shear stress / type II transforming growth factor beta receptor binding / type I transforming growth factor beta receptor binding / mammary gland development / cell-cell junction organization / digestive tract development / transforming growth factor beta binding / face morphogenesis / odontogenesis / Molecules associated with elastic fibres / positive regulation of filopodium assembly / lung alveolus development / TGF-beta receptor signaling activates SMADs / inner ear development / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of SMAD protein signal transduction / positive regulation of cell division / ECM proteoglycans / positive regulation of collagen biosynthetic process / positive regulation of epithelial to mesenchymal transition / salivary gland morphogenesis / positive regulation of stress fiber assembly / T-tubule / transforming growth factor beta receptor signaling pathway / platelet alpha granule lumen / response to progesterone / female pregnancy / cytokine activity / positive regulation of protein secretion / negative regulation of transforming growth factor beta receptor signaling pathway / growth factor activity / response to estrogen / Platelet degranulation / regulation of cell population proliferation / collagen-containing extracellular matrix / in utero embryonic development / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / response to hypoxia / positive regulation of apoptotic process / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / neuronal cell body / positive regulation of cell population proliferation / protein-containing complex binding / positive regulation of DNA-templated transcription / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / molecular replacement / Resolution: 2 Å | |||||||||
Authors | Mittl, P.R.E. / Priestle, J.P. / Gruetter, M.G. | |||||||||
Citation | Journal: Protein Sci. / Year: 1996 Title: The crystal structure of TGF-beta 3 and comparison to TGF-beta 2: implications for receptor binding. Authors: Mittl, P.R. / Priestle, J.P. / Cox, D.A. / McMaster, G. / Cerletti, N. / Grutter, M.G. #1: Journal: J.Mol.Biol. / Year: 1993 Title: Refined Crystal Structure of Human Transforming Growth Factor Beta 2 at 1.95 A Resolution Authors: Schlunegger, M.P. / Grutter, M.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tgj.cif.gz | 37.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tgj.ent.gz | 24.7 KB | Display | PDB format |
PDBx/mmJSON format | 1tgj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/1tgj ftp://data.pdbj.org/pub/pdb/validation_reports/tg/1tgj | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12734.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ONE DIOXANE MOLECULE BOUND / Source: (gene. exp.) Homo sapiens (human) Description: STRAIN DEPOSITED AT DEUTSCHE SAMMLUNG VON MIKROORGANISMEN, MASCHENRODER WEG 1B, 3300 BRAUNSCHWEIG, GERMANY, ACCESSION NUMBER IS DSM 5658 Gene: HTGF-BETA3 / Plasmid: PPLMU / Gene (production host): HTGF-BETA3 / Production host: Escherichia coli (E. coli) / Strain (production host): LC137 / References: UniProt: P10600 |
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#2: Chemical | ChemComp-DIO / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | THE PROTEIN WAS CRYSTALLIZED FROM A SOLUTION CONTAINING 15 % DIOXANE. ONE DIOXANE MOLECULE IS BOUND ...THE PROTEIN WAS CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 43.37 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: 15% (V/V) DIOXANE, 100 MM SODIUM ACETATE, PH 5.0 | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Dec 16, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 6323 / % possible obs: 76 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 |
Reflection shell | Resolution: 2→2.1 Å / Rmerge(I) obs: 0.353 / % possible all: 37.4 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 10 Å |
Reflection shell | *PLUS % possible obs: 37.4 % |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: TGF-BETA2 (SCHLUNEGGER & GRUETTER) Resolution: 2→7 Å / σ(F): 0
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Displacement parameters | Biso mean: 29.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.1 Å / % reflection obs: 37.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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