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- PDB-1kth: The Anisotropic Refinement Of Kunitz Type Domain C5 at 0.95 Angstrom -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kth | ||||||
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Title | The Anisotropic Refinement Of Kunitz Type Domain C5 at 0.95 Angstrom | ||||||
![]() | Collagen alpha 3(VI) chain | ||||||
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Function / homology | ![]() collagen type VI trimer / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / Signaling by PDGF / NCAM1 interactions / muscle organ development / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / ECM proteoglycans ...collagen type VI trimer / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / Signaling by PDGF / NCAM1 interactions / muscle organ development / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / ECM proteoglycans / Integrin cell surface interactions / response to glucose / response to UV / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Arnoux, B. / Ducruix, A. / Prange, T. | ||||||
![]() | ![]() Title: Anisotropic behaviour of the C-terminal Kunitz-type domain of the alpha3 chain of human type VI collagen at atomic resolution (0.9 A). Authors: Arnoux, B. / Ducruix, A. / Prange, T. #1: ![]() Title: The 1.6 A structure of Kunitz-Type domain from the alpha 3 chain of human type VI collagen. Authors: Arnoux, B. / Merigeau, K. / Saludjian, P. / Norris, F. / Norris, K. / Bjorn, S. / Olsen, O. / Petersen, L. / Ducruix, A. #2: ![]() Title: 1.2 A Refinement of the Kunitz Type Domain from the alpha3 Chain of Human Type VI Collagen. Authors: Merigeau, K. / Arnoux, B. / Perahia, D. / Norris, K. / Norris, F. / Ducruix, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 38.7 KB | Display | ![]() |
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PDB format | ![]() | 25.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2kntS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 6639.508 Da / Num. of mol.: 1 / Fragment: Kunitz-type Domain C5, C-Terminus Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.55 Å3/Da / Density % sol: 36.38 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.4 Details: phosphate buffer, sodium sulfate, pH 3.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 K / pH: 3 / Method: vapor diffusion, sitting drop / Details: Arnoux, B., (1995) J. Mol. Biol., 246, 609. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 1998 |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 0.95→8 Å / Num. all: 28107 / Num. obs: 22448 / % possible obs: 90.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 0.95→0.97 Å / Rmerge(I) obs: 0.051 / Num. unique all: 1598 / % possible all: 85.2 |
Reflection | *PLUS Highest resolution: 0.95 Å / Num. obs: 33572 / % possible obs: 95.2 % / Num. measured all: 179075 / Rmerge(I) obs: 0.041 |
Reflection shell | *PLUS Rmerge(I) obs: 0.34 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2KNT Resolution: 0.95→5 Å / Num. parameters: 5097 / Num. restraintsaints: 6007 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-22 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 551.81 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→5 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 0 / Num. reflection Rfree: 1147 / % reflection Rfree: 6 % / Rfactor all![]() ![]() ![]() | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_plane_restr / Dev ideal: 0.041 |