+Open data
-Basic information
Entry | Database: PDB / ID: 5vt2 | ||||||
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Title | Crystal structure of growth differentiation factor | ||||||
Components | Growth/differentiation factor 15 | ||||||
Keywords | SIGNALING PROTEIN / TGF-beta family | ||||||
Function / homology | Function and homology information negative regulation of growth hormone receptor signaling pathway / reduction of food intake in response to dietary excess / glial cell-derived neurotrophic factor receptor signaling pathway / SMAD protein signal transduction / negative regulation of multicellular organism growth / positive regulation of myoblast fusion / transforming growth factor beta receptor signaling pathway / cytokine activity / growth factor activity / cell-cell signaling ...negative regulation of growth hormone receptor signaling pathway / reduction of food intake in response to dietary excess / glial cell-derived neurotrophic factor receptor signaling pathway / SMAD protein signal transduction / negative regulation of multicellular organism growth / positive regulation of myoblast fusion / transforming growth factor beta receptor signaling pathway / cytokine activity / growth factor activity / cell-cell signaling / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Golgi apparatus / signal transduction / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Min, X. / Wang, Z. | ||||||
Citation | Journal: Sci Transl Med / Year: 2017 Title: Long-acting MIC-1/GDF15 molecules to treat obesity: Evidence from mice to monkeys. Authors: Xiong, Y. / Walker, K. / Min, X. / Hale, C. / Tran, T. / Komorowski, R. / Yang, J. / Davda, J. / Nuanmanee, N. / Kemp, D. / Wang, X. / Liu, H. / Miller, S. / Lee, K.J. / Wang, Z. / Veniant, M.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vt2.cif.gz | 58.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vt2.ent.gz | 41.4 KB | Display | PDB format |
PDBx/mmJSON format | 5vt2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/5vt2 ftp://data.pdbj.org/pub/pdb/validation_reports/vt/5vt2 | HTTPS FTP |
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-Related structure data
Related structure data | 2r52S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12303.248 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GDF15, MIC1, PDF, PLAB, PTGFB / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q99988 #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
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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: 4.24 Å3/Da / Density % sol: 70.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 15% w/v Tascimate, pH 7.0, 0.1 M HEPES, pH 7.0, 2% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9793 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 27, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.282→40.139 Å / Num. obs: 19823 / % possible obs: 99.8 % / Redundancy: 5 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.09 / Rsym value: 0.08 / Net I/av σ(I): 6.4 / Net I/σ(I): 11.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2R52 Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.987 / SU ML: 0.141 / SU R Cruickshank DPI: 0.1871 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.173 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.4 Å2 / Biso mean: 52.322 Å2 / Biso min: 28.87 Å2
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Refinement step | Cycle: final / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.282→2.341 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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