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Open data
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Basic information
Entry | Database: PDB / ID: 2knt | ||||||
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Title | THE 1.2 ANGSTROM STRUCTURE OF KUNITZ TYPE DOMAIN C5 | ||||||
![]() | COLLAGEN | ||||||
![]() | KUNITZ INHIBITOR / EXTRACELLULAR MATRIX / CONNECTIVE TISSUE | ||||||
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 / phosphatidylinositol 3-kinase/protein kinase B signal transduction / extracellular matrix / serine-type endopeptidase inhibitor activity / sarcolemma / extracellular vesicle / neuron apoptotic process / collagen-containing extracellular matrix / cell adhesion / endoplasmic reticulum lumen / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Merigeau, K. / Arnoux, B. / Ducruix, A. | ||||||
![]() | ![]() 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 | ![]() | 23.4 KB | Display | ![]() |
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PDB format | ![]() | 15.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 396.7 KB | Display | ![]() |
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Full document | ![]() | 396.9 KB | Display | |
Data in XML | ![]() | 3.5 KB | Display | |
Data in CIF | ![]() | 4.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1aapS 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: DOMAIN C5, C-TERMINUS OF TYPE VI COLLAGEN Source method: isolated from a genetically manipulated source Details: KUNITZ-TYPE / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 39 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 3.3 Details: 0.2M LI2SO4, 0.1M CITRIC ACID, 0.074M NA2HPO4, 1.6M (NH4)2SO4, 10MG/ML, PH3.3 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / 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: 291 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 14, 1995 |
Radiation | Monochromator: YES / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.901 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→20.4 Å / Num. obs: 16657 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 46.5 |
Reflection shell | Resolution: 1.18→1.21 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.09 / Rsym value: 0.75 / % possible all: 52.5 |
Reflection | *PLUS Num. measured all: 84000 |
Reflection shell | *PLUS % possible obs: 61 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AAP Resolution: 1.2→7 Å / Num. restraintsaints: 5876 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: BABINET | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 630 / Occupancy sum non hydrogen: 476 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→7 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-93 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 10762 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |