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Yorodumi- PDB-4iua: Crystal Structure of the NK2 Fragment (31-290) of the mouse Hepat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iua | ||||||
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Title | Crystal Structure of the NK2 Fragment (31-290) of the mouse Hepatocyte Growth Factor/Scatter Factor | ||||||
Components | Hepatocyte growth factor | ||||||
Keywords | HORMONE / HGF/SF / KRINGLE domain / GROWTH FACTOR | ||||||
Function / homology | Function and homology information positive regulation of neuron projection regeneration / MET Receptor Activation / Drug-mediated inhibition of MET activation / MET interacts with TNS proteins / MET activates STAT3 / MET activates PI3K/AKT signaling / MET activates RAS signaling / MET activates PTPN11 / MET activates PTK2 signaling / MET activates RAP1 and RAC1 ...positive regulation of neuron projection regeneration / MET Receptor Activation / Drug-mediated inhibition of MET activation / MET interacts with TNS proteins / MET activates STAT3 / MET activates PI3K/AKT signaling / MET activates RAS signaling / MET activates PTPN11 / MET activates PTK2 signaling / MET activates RAP1 and RAC1 / MET receptor recycling / Negative regulation of MET activity / RAF/MAP kinase cascade / regulation of p38MAPK cascade / positive regulation of myelination / PIP3 activates AKT signaling / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Platelet degranulation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / skeletal muscle cell proliferation / negative regulation of hydrogen peroxide-mediated programmed cell death / hepatocyte growth factor receptor signaling pathway / myoblast proliferation / cellular response to hepatocyte growth factor stimulus / positive regulation of DNA biosynthetic process / negative regulation of release of cytochrome c from mitochondria / chemoattractant activity / negative regulation of interleukin-6 production / positive regulation of interleukin-10 production / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of peptidyl-serine phosphorylation / cell chemotaxis / liver development / epithelial cell proliferation / growth factor activity / cell morphogenesis / negative regulation of inflammatory response / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / positive regulation of protein phosphorylation / signaling receptor binding / protein-containing complex binding / negative regulation of apoptotic process / proteolysis / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å | ||||||
Authors | Tolbert, W.D. / Zhou, E. / Kovach, A. / Melcher, K. / Xu, H.E. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the NK2 Fragment of the mouse Hepatocyte Growth Factor/Scatter Factor Authors: Tolbert, W.D. / Zhou, E. / Kovach, A. / Melcher, K. / Xu, H.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iua.cif.gz | 827.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iua.ent.gz | 692.3 KB | Display | PDB format |
PDBx/mmJSON format | 4iua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/4iua ftp://data.pdbj.org/pub/pdb/validation_reports/iu/4iua | HTTPS FTP |
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-Related structure data
Related structure data | 3hn4S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 30414.326 Da / Num. of mol.: 8 / Fragment: NK2 fragment (UNP residues 31-290) / Mutation: C215A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hgf / Plasmid: PET-DUET1/MBP-TRX / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI B(DE) / References: UniProt: Q08048 #2: Chemical | ChemComp-EPE / #3: Chemical | ChemComp-SO4 / |
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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: 3.14 Å3/Da / Density % sol: 60.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 200 mM ammonium sulfate, 18% PEG 4000, 200 mM HEPES pH 7.0, 5% 2-METHYL-2,4-PENTANEDIOL, 0.5 mM beta-octyl glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1271 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 16, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.05→30 Å / Num. all: 57781 / Num. obs: 57775 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 13.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HN4 Resolution: 3.05→29.775 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 25.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.05→29.775 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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