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- PDB-7ocl: K1K1, a potent recombinant minimal hepatocyte growth factor/scatt... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ocl | ||||||
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Title | K1K1, a potent recombinant minimal hepatocyte growth factor/scatter factor mimic | ||||||
![]() | Hepatocyte growth factor alpha chain,Hepatocyte growth factor alpha chain | ||||||
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Function / homology | ![]() positive regulation of neuron projection regeneration / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / regulation of p38MAPK cascade / Drug-mediated inhibition of MET activation / MET activates STAT3 / skeletal muscle cell proliferation / negative regulation of hydrogen peroxide-mediated programmed cell death / positive regulation of myelination / MET interacts with TNS proteins / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | de Jonge, H. / de Nola, G. / Gherardi, E. | ||||||
![]() | ![]() Title: Dimerization of kringle 1 domain from hepatocyte growth factor/scatter factor provides a potent MET receptor agonist. Authors: de Nola, G. / Leclercq, B. / Mougel, A. / Taront, S. / Simonneau, C. / Forneris, F. / Adriaenssens, E. / Drobecq, H. / Iamele, L. / Dubuquoy, L. / Melnyk, O. / Gherardi, E. / de Jonge, H. / Vicogne, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.1 KB | Display | ![]() |
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PDB format | ![]() | 108.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.2 KB | Display | ![]() |
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Full document | ![]() | 433.2 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 23.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19232.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.74 % / Description: Hexagonal shaped |
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Crystal grow![]() | Temperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM Tris/Bicine pH 8.5, 30 mM Sodium nitrate, 30 mM Sodium phosphate dibasic, 30 mM Ammonium sulfate, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD Temp details: Inside fridge-like incubator |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 10, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.61→43.29 Å / Num. obs: 42914 / % possible obs: 99.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 20.25 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.074 / Rrim(I) all: 0.172 / Net I/σ(I): 4.6 / Num. measured all: 224081 / Scaling rejects: 25 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: Kringle 1 Resolution: 1.8→43.29 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.64 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.21 Å2 / Biso mean: 32.9721 Å2 / Biso min: 10.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→43.29 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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